Perception is for observation, Investigation is for deduction.

Some of this answer will be observations on how Wizards has done it so far and some of this will be logic, and some of it will be mechanics.

First for the headline question. It depends. when to use Investigation, and when to use Perception is not entirely clear yet, and I'm hoping we'll get more guidance in the DMG late this year. The guidance from the rules is that the two skills mostly seem to differ in the methods by which they are found.

Depending on the exercise, either, or both of the skills may be used.

For passive checks, you're almost always looking at Perception being the skill of record. While all skills can be used passively, some skills make more sense than others. Perception is the hallmark passive skill, whereas investigation makes less sense as a passive skill.

If the character is alert to the possibility of hidden objects/traps, but not actively searching, he's using passive perception.

The guidance for this seems to be (though we can't confirm yet), that the DC for actively looking for something is regularly about 5 less than the DC for passively looking for something (or sometimes actively looking always reveals it).

So here's how I would play it. Traps can be noticed with perception passively (usually DC 15). If the PC is looking, ask them how they are looking. If it's observational, then use Perception. If it's deductive, use Investigation. When they are searching for items, again, either skill is appropriate. This is somewhat counter to how WOTC has written adventures so far. They are always written to use perception to notice traps. Passive with a higher DC and active with a lower.

Investigation also has broader uses such as when you are trying to track clues, or put something together. It's also a great "roll for a hint" kind of skill if your PCs get stuck and need some help figuring out what to do next.

RAW the Rogue does receive the benefits of Expertise to his passive.

A passive check is a special kind of ability check that doesn’t involve any die rolls. Such a check can represent the average result for a task done repeatedly, such as searching for secret doors over and over again, or can be used when the DM wants to secretly determine whether the characters succeed at something without rolling dice, such as noticing a hidden monster. Here’s how to determine a character’s total for a passive check: 10 + all modifiers that normally apply to the check. - Player's Handbook P.174

The player has invested in making this character good at this, this is not a bad thing.

Rogues in general are supposed to be good at this type of thing, hence the proficiency bonus class feature and the player specifically spent a feat on making his passive perception better. The player could've spent this on another feat to specialize in another area (or gain a combat ability). This is a good thing, while it may make it difficult for the Rogue to be surprised by a trap or an ambush you should in no way try to outmaneuver this.

Don't worry, there are downsides to the Rogue for this.

To reliably spot traps and ambushes the rogue will need to be at the head of the marching order so that he has clear sight lines. Rogue's are not particularly hardy and the party as a whole is inviting more risk for this reward. Likewise while he is extremely excellent at spotting physical dangers, the Rogue will not be able to detect magic wards and other dangerous enchantments and may equally blunder into them.

Ways to handle his detection of a trap or an ambush

You are correct in assuming that only that PC has seen the trap/enemy. Unless he has some mode of telepathic communication he will need to speak out and announce the threat to everyone. The best way to handle this sort of thing is to pass notes or send text messages to the player(s) able to see/detect the issue and leave it to them to react and tell someone else. Intelligent enemies will see/hear the rogue warning the party and the combat should start immediately (no surprise round though).

The PC does not become omniscient of the trap upon detecting it.

The PHB itself is very, very vague on what information is received when a PC detects a trap. However, the DMG does have a nice little section about traps, their detection, and disarming them:

If the adventurers detect a trap before triggering it, they might be able to disarm it, either permanently or long enough to move past it. You might call for an Intelligence (Investigation) check for a character to deduce what needs to be done, followed by a Dexterity check using thieves' tools to perform the necessary sabotage...

...In most cases, a trap's description is clear enough that you can adjudicate whether a character's actions locate or foil the trap. As with many situations, you shouldn't allow die rolling to override clever play and good planning...

...Foiling traps can be a little more complicated. Consider a trapped treasure chest. If the chest is opened without first pulling on the two handles set in its sides, a mechanism inside fires a hail of poison needles toward anyone in front of it. After inspecting the chest and making a few checks, the characters are still unsure if it's trapped. Rather than simply open the chest, they prop a shield in front of it and push the chest open at a distance with an iron rod. In this case, the trap still triggers, but the hail of needles fires harmlessly into the shield. - Dungeon Master's Guide p. 121

Essentially though whether trap disarming is simply a dex check, a series of checks, and/or involves serious RP is up to you as a DM. I would encourage the open-ended approach the book suggests as it adds complexity and makes trap checking and disarming a more engaging process. Sitdown with the party OOC and discuss what the table as a whole thinks should happen for trap checks and move forward based on that consensus.