As far as I am aware, there is no way to give a creature the incapacitated condition directly. However, there are 4 conditions that give a creature the incapacitated condition as part of their effects. These are:
- Paralysed
- Petrified
- Stunned
- Unconscious
There are a number of ways to apply these conditions without damaging your beloved pet. Within the Warlock spell list, the ones I could find are:
- Hypnotic Pattern
- Hold Monster
- Eyebite
- Flesh to Stone
- Power Word Stun
- Imprisonment
However, only Flesh to Stone, Imprisonment and Power Word Stun last longer than 1 minute. Flesh to Stone is severely not recommended, since you really shouldn't be able to harvest posion from a statue. Imprisonment is expensive, but will work well for this task. Power Word Stun is probably the best option, since your creature can choose to fail its saving throws till you're finished.
On the other hand, if you have an allied Bard, Cleric, or Wizard, the 3rd-level spell Feign Death suits your needs perfectly. It will give a willing creature the incapacitated condition for an hour. A Cleric wouldn't even need to waste a spell learning it, since Clerics know all their spells automatically. Since it's a ritual, he wouldn't even need to waste a spell slot on casting it! All you have to do is talk him into preparing it.
Of course, all this is moot if your DM is willing to allow you to extract poison simply on the basis that your wyvern is tame and willing to allow you to do what you want to it. Given that he's giving you a CR 6 creature for a mount, a little bit of poison is really not a big deal.
TL;DR: Spell scroll is a consumable item. It holds a spell which can be cast from it or copied into a wizard's spellbook, both of which destroy the scroll. Spell on a scroll refers to that specific spell, which is incidentally written on a scroll.
Spell scrolls (as you'd find in the treasure tables) are spells already prepared onto the scroll and contain some/all of the magic needed to cast them within them (which is why creating them is more than just copying things out of a book).
The second passage you are quoting describes how wizards copy any spell that they find written on a piece of parchment, in a book or on the back of a box of your favourite Orcish breakfast cereal, and put it into their spellbook.
Copying a Spell into the Book. When you find a wizard spell of 1st level or highter, you can add it to your spellbook if its of a level for which you have spell slots and if you can spare the time to decipher and copy it.
Copying a spell into your spellbook involves reproducing the basic form of the spell, then deciphering the unique system of notation used by the wizard who wrote it. You must practice the spell until you understand the sounds or gestures required, then transcribe it into your spellbook using your own notation.
The rules in the DMG are specifically about spells on spell scrolls (the type found in the random treasure tables etc.)
In addition to the rules on copying any spell into your spellbook you also have to follow these rules specific to spell scrolls.
A wizard spell on a spell scroll can be copied just as spells in a spellbook can be copied. When a spell is copied from a spell scroll, the copier must succeed on an Intelligence(Arcana) check with a DC equal to 10 + the spell's level. If the check succeeds, the spell is successfully copied. Whether the check succeeds or fails, the spell scroll is destroyed.
Basically you get one shot to understand enough about this spell scroll before the magic is used up and you can't copy it into your book.
So yes, there's a difference between a plain written spell on any old piece of parchment, and a spell scroll.
Additionally: As KorvinStarmast brought up in the comments you could have someone else help you with this check using the Help action.
Help
You can lend aid to another creature in the completion of a task. When you take the Help action, the creature you aid gains advantage on the next ability check it makes to perform the task you are helping with, provided that it makes the check before the start of your next turn.
Bare in mind that many DMs rule that you can only help with tasks that it makes sense for you to be able to aid someone with. In this instance I would think that at the very least they'd need to have the spell in question on their own class's spell list, or perhaps even be a wizard themselves.
Best Answer
Yes, there's a difference
A creature is the superset of that contains monsters. As proof, consider the player characters themselves: they are creatures, clearly, but they are not monsters. Monsters are what you throw at the player characters so they can fight it and maybe kill it.
For specific spells which seem to equate "monster" and "creature" together: note that using a harmful spell against someone, like dominate monster, is an inherently adversarial act. Casting a harmful spell (that is meant to target monsters) at a creature is an act of fighting it, thereby putting that targeted creature into the basket of "monster."
It isn't a very useful distinction
To separate creatures from monsters strictly isn't too useful, if you accept that anyone that the PCs battle is moved to the basket of "monster," because the members of that "monster" set can change. A more useful distinction would be PC vs NPC, protagonist vs antagonist, or ally vs enemy.