So one issue I am having at the moment is I am trying to figure out the CR of skill checks, and what said CRs will be. Now I'm not talking about PCs using a knowledge skill to identify a monster--the information they gain is reward enough and built into the monster should they try to extract it--but more of lock-picking DCs and the amount of XP the person defeating it should get.
So something like
DC x = CR Y with 1/4 the xp going to the single PC.
Does my question make sense?
Your question does make sense, but the game doesn't assume that standard skill checks (like picking a lock) are going to give XP, unless maybe said lock is necessary to complete the quest and get quest XP.
Generally, XP is only given for combats, traps, and story. Skill checks, unless they're necessary for one of those things, don't give XP.
Johnico is right, there isn't a system to reward players for successful skill checks. They're usually apart of combat, or succeeding in a quest which results in Story Experience.
Also, don't ever apply experience anything but equally between PCs in a part. Rewarding the Rogue for picking a lock isn't fair unless you're going to specially reward a wizard when he casts a utility spell or a fighter when he takes a hit. It's all "part of the job". Especially, when you as a GM are the one who sets up the challenges and rewards, you'll basically be choosing to reward one player more than the others. If that's what you want to do, don't make a farce of it by pretending it's fair to reward one character and not others.
So I think how I would run this is to make these "bypasses" into traps.
It is odd having traps that use different skills than Perception and Disable device, but at their core everything can be boiled down to a "Notice" like skill followed by a "Resolve" skill,
E.G.
Sense Motive and Diplomacy (Realize Char X is holding something back, and then convince him to help you)
Perception and Climb (Notice the hole in the ceiling, and climb into it without collapsing it or in some way triggering it to close)
In short the design works like this:
Since DC 30 "notice" and DC 30 "resolve" makes a CR 6 trap it would give XP for a CR 6 encounter to the party if they succeeded, but would reward no loot.
So:
Bypass (CR 6)
This "trap" isn't so much a trap as a way to avoid danger. Often placed in ambush areas, this enables the PCs to "skip ahead" to a different part of the dungeon or module for a similar amount of XP. Failure acitvates a cantrip (probably Open/Close) that closes the bypass and creates a loud enough boom to alert the encounter that the Bypass evades.
Success:
Party gains CR 6 XP for defeating the bypass, and skips ahead to bypass's exit.
Failure:
Either the party rolls initiative, and enemies forming the encounter attack the party, OR they are denied the bypass and must now contend with the encounter ahead.
Ideas:
A bypass that skips an underwater encounter with Bloody Owlbear Skeletons.
A bypass that is surrounded by zombies that the PCs cannot see--but likewise the zombies cannot see them. When the bypass is failed the zombies are alerted to the PCs presence and attack.
Bypasses would be designed to use every single skill that a Cleric, Fighter, Rogue, and Wizard would have.
A spellcraft check required to activate a magic-mouth which cryptically speaks to the PCs, and a linguistics check required to figure out the riddle or decipher the password from what the Magic Mouth is saying.
I want to make these "useless" skills more useful so people second guess making uber-powerhouses. If one person is playing a god gish of facerolling then that is great, but if everyone is playing that then nothing will stand in their way.
On top of that I want my rogue players to feel like they have a reason for being in the party aside from being the one that traps kill first.