Well, this is a great question, and I must say beforehand that my experience with an organization of villains is pretty narrow. But I do hope that what I'll write here might be of some use to you.
Inspiration
One of the key things that you can do is to find inspiration for your villains in other sources. I once based an organization of villains around the 7 exes from Scott Pilgrim vs the World. Another time it was around a bunch of villains from westerns. The trick is to find some villains that are cool and draw inspiration from them.
This inspiration can be in terms of copying the villains, or it can be in terms of taking certain parts of their personalities. It can even mean analyzing what made them so memorable and using that someway.
Make them somewhat related to the characters
You want your players to care for them, to remember them, or something around those lines. For that, you have to make them related somehow to the PCs. While having them compete for the same goal is nice, I do prefer something closer to the trick utilized in Scott Pilgrim, having them the exes of a certain friend, relative or the like. Maybe have some of them be immediate family of the PCs? A true connection is far better in order to make the players care for them enough to hate them, love them, or even love to hate them.
Make each one of them unique
This is also very important. While they are all a part of an evil organization, they must be unique by themselves. Each and every one of them is also a villain that the party will have to encounter one day or the other. In Hot Fuzz each one of the conspiracy members is unique and is colorful enough to be remembered. We have the couple who hate the reporter for stating the wife's age is higher than it really is. We have the farmer whose mother has a rifle. We have the chief of police who doesn't punish criminals and we have the manager of the Supermarket who is always there when you least expect him. In Scott Pilgrim we have the Female ex who Ramone experimented with, we have the actor who has doubles, we have the leader who is an agent and who can control Ramona and so many more.
Go for it too, make them unique, make them colorful, make them come alive as persons and not only is a part of an organization. The fact The Joker fights sometimes alongside with Bane doesn't make each one of 'em less frightening, unique or evil, right? Why should that be the case here?
Have something common for all of them
Being unique doesn't mean that they have to be completely different. In Scott each of the exes is an ex of Ramona, and an idiot. In Angel they are all attorneys. In the first and second seasons of Buffy they're all vamps. Have something that unites the villains that is common to all of them. Maybe all of them have similar clothes or use the same perfume? Maybe they all talk a bit funny?
As a bonus, if you can make the uniting thing a thing that is cool and all by itself, which can make alone the villain stand out, it is even better.
Let the players know of them in advance
The characters should know about the organization pretty early, but having the players know about the organization even earlier can do magic sometimes to your campaign. If they'll know that their characters will fight an organization of villains, the players will look for them (and with far greater anticipation). Always remember that the players are authors as well as audience, and if they will be looking forward to meeting the villains they will far better enjoy this meeting between their characters and villains. But they will also search for them; lead their characters to them, and so much more.
Addendum
I also highly recommend reading answers to questions like these two. While they do center on creating a single villain, they are still quite useful and in more than just creating and fleshing each and every one of the villains in the organization.
A group 3rd- to 5th-level PCs in B/X and compatible games can defeat NPCs 2 to 3 levels higher than the PCs, and maybe even NPCs of higher levels than that if the PCs scout ahead, plan the engagement, possess the necessary equipment, and have the element of surprise. Remember that one-shot magic items such as scrolls and potions can vastly amplify the party's capabilities!
Obviously, in a straight-up fight, the PCs would surely lose (except at my table where I always roll poorly for bosses yet exceptionally well for their weak underlings). PCs should be given fair warning about the possibility of their own defeat. If the PCs can't knock down the NPC quickly, the NPCs will retaliate, and that could result in the death of a PC or two, but that's possible against evenly matched foes, so it's not really that big of a deal.
Best Answer
Build a criminal network as your BBEG
I have had success over the years in using the Organized Crime family model (an example is mentioned here) to provide scalable challenges to parties of good, neutral, and evil/chaotic alignments. The emphasis is on rivalry as the tension builder between your PCs and their nemesis.
What are the advantages of doing this?
As you may be familiar from the real world, organized crime families won't necessarily ally with other organized crime groups (drug cartels, mafia families) just because they are criminal (or if we like, for D&D purposes, just because they are Evil). They will fight with, ally with, or take over other crime organizations based on their goals, motives and opportunities.
The layered network of the criminal organization lends itself to a steadily increasing CR/challenge for your PCs with a logical "final" boss/group of pretty high CR. (Having the whole thing masterminded from the shadows by a demon, a vampire, or an evil dragon fits the D&D Swords and Sorcery genre).
Your PCs are a criminal gang, as described.
Their goal is to take over. At least one other organized crime group is either in charge, or wants to take over. They are not intetested in being recruited just because "we are evil" but rather, they have their own goals and motives for wishing to take over the world, just as your PC's do.
As a campaign plot element, you can have the larger Criminal Organization recruit your players while they are at low levels, then as the PCs gain levels the rivalry begins to take shape. That approach is a trope that can be seen in a lot of Hollywood films, TV shows, books, and other entertainment media1.
Scalable challenges
As with various herirachical organizations, criminal and otherwise, your PCs will encounter the low level foot soldiers (guards, thugs, bandits, Knights, etc) before they run into the tougher NPC's like:
ArchMage (CR 12) with minions;
A few Champions (CR 9 warrior type, Volo's Guide to Monsters) with squads of soldiers/archers/scouts serving them,
Allied giants, mind flayers, or other monsters who share the goals of the crime family, or are allied for their own reasons.
A vicious cabal of halfling thieves, assassins, bards, and sorcerers such as those encountered by Finieous Fingers and his crew.
Quantity has a quality all its own
If you go through your encounter creation steps in the DMG, or in the Basic Rules, pages 165-166, you'll notice that even low level CR NPCs (Bandits, Pirates, Thugs, Scouts, Guards, Knights) can in medium to large sized groups create deadly encounters at varying PC levels due to the number of attacks per round that your PCs are subjected to. Ranged attacks: use them!
Let's use 4 Knights as an example encounter.
4 CR 3 Knights x 700 = 2800, multiplied by 2 for being between 3-6 enemies. For a party of 4 6th level characters, that's Deadly encounter. (5,600 XP Threshold, Basic Rules, p. 165). Granted, the encounter math is an estimate. Tossing in an Acolyte or a Cult Fanatic to support them with spells may make the encounter a lot more difficult ...
Match your capstone encounters (or your late-tier tier 1, tier 2, and tier 3 major encounters against the party's level as they peel the layers back to expose the deeper and more dangerous enemies who are an obstacle to their long term success in taking over.
1 FWIW, Waterdeep Dragon Heist has a reasonable illustration of the criminal organization model in a published setting, but you don't need to buy that book to pull this off. The CRPG Baldur's Gate has the BBEG use economic groups and other adventuring parties to stop the protagonist's party.
If the PCs try to recruit the antagonists, a remedy for this is to role-play those NPCs into situations where they frequently and routinely betray the PCs. With a few exceptions, evil characters are typically self-serving. (thanks @R.McMillan)