or will it hurt/stuff something up?

and also

if you have two active pickups in your guitar do you need to have 2 batterys or just one ?
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Esp Ltd EC100QM
Esp Ltd EC1000 Deluxe

Randall RG100G3
Randall 2x12 Extension Cab

Zoom 9.2tt
One battery, and it is perfectly acceptable to have the battery in that compartment if you have enough room.
Yes it can go in with the electronics. To the other questions you only need one battery, but there is a thing called the 18V mod where you run 2 batteries and alot of people say it really improves tone. Also if your only amp is the one in your sig I would avoid actives. Actives+SS amps=/= good tone.
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if you have enough room.

Big if...no way a battery could fit in any of my guitars. You could always make more space yourself if you wanted.