So from what I understand, you know for a fact that one of the two employees stole the money, but are afraid to confront them because you and they are working on a time-limited project? Then, I'd say keep your money with you all the time and fire BOTH of them when your project is over and you're not dependant on them. By the way, there's no way just one of them is stealing the money, it has to be both of them. No way one could steal the money from a wallet from a bag in the same room, without the other one noticing.
Here's what you do, line both up for a "meeting". Look both in the eye, make a sudden punch towards both, and fire the one who moves first.
i think you used the money, and u forgot where u spent them, becuase i dont think they will take 5% they will take them all.
I sleep in another room, but put bags in which wallets is in office room. The method is creative, but not accurate. It depends on many factors? if they stole all, i will found that, he/she will be fired definitely. it is right to put my money in safe way. but how to handle the thief? take it normal, and let it be? or think it is definitely wrong thing, and fire him/her? Yes, it is possible. But it is possible too that one stole money when another go to WC or go out for lunch or break.