NEED CHINCHILLA HELP?

i have 2 chinchillas and they are 5 months old, they are very big now, but the only problem is they hate me. the smaller chinchilla, when i try picking him up to take him out so i can clean the cage, hes more boney then the other one. i feel like im hurting them they squeel and they go to the corner of the cage and try to hide. i dont let them run around a room, im afraid theyll get lost or go behind a piece of funitire i can not get inback of, are they always going to be like this??? i try to care for them so much but im about to just give up, i even bought them a wheel and they never use it, I NEED HELP!!!!!!!!!!!!!!!!!!!!!!!!!