The third floor with bedrooms is largely extra space. The two labeled as bedrooms are all ready furnished as guest rooms. The owner's suite is largely for storage, but can be converted to a bedroom if need be. The bonus room is Helena's lab/work area.
Bedroom One: Steve Bedroom Two: Pete
Now as for all the hidden nooks. In Helena's room, her bookcase opens to reveal a small hidden room where she kept most of her Agent-related things she'd need while in the field tracking an artifact. There is a similar hidden room in the library on the main floor where Helena kept most of her gadgets and such (aka where she kept the Imperceptor Vest, which is actually there, but it has no antimatter to power it so it is basically useless). Each bedroom most likely has a similar hidden panel/room in it.
Now for the traps. There are anti-gravity traps in the library, main entryway, and each bedroom. There's probably some sort of Tesla-like trap also in the library to protect some of her valuable papers/whatever she has in a safe behind a hidden panel, and another Tesla-like trap in the bonus room protecting her inventions/notes on said inventions that are kept in a safe. The anti-gravity traps are triggered by flipping a switch (see the Warehouse 13 season 2 episode 1 "Time Will Tell" for what the switches look like in the house). The Tesla traps are tripped when one tries to forcibly open the safe or gets the code to it wrong, and are stun-only, not vaporize.
Helena would inform anyone living with her where all the traps/triggers are so they aren't accidentally triggered. Given that all the switches for the anti-gravity traps are hidden in wall panels, no one visiting would be in danger of accidentally triggering the trap. Unless they somehow activated the wall panel to move and reveal the switch and pull it without Helena noticing.
If your character is moving in, comment here with what bedroom they are taking! This is also posted in Helena's journal and may soon be added to when Helena gets around to asking about magically adding a level to the house. Because uh...she's running out of bedrooms for the Warehouse gang.