Someone using or stealing your items without asking is an issue that needs to be taken care of immediately, especially in the case of personal belongings. The best way to handle the problem is by confronting your roommate about it.
If you want to get the truth out of someone, you have to discuss issues like this in a casual matter. Don't act like you're really mad or upset (even if you are) because if you startle them, they may put up their guard and not be as open to making a compromise or having a conversation about the issue.
Start by saying something like, "I noticed that I had less cereal than I thought, did you have any?" If you beat around the bush and your roommate still won't confess, give it a few days to see if they stop after your questioning.
If the sneaking around doesn't stop, you need to have a serious conversation. Sit your roommate down and say that you really want to have a good relationship with them, which means honesty and trust. Tell them that you noticed that your items have been missing, stained, changed or misplaced, and use specific examples. Tell them that unless they have been leaving the door unlocked, you're not sure who else it could possibly be.
Also, let them know that if they want to use something, they should ask. Tell them that you have enough respect for them to leave their things alone while they are not in the room, and that you expect the same in return.
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