Basically, you can use any of them as you wish. HOWEVER, you may realize 'Hanya' is commonly used in books, letters, newspapers and etc (formal);people no longer use Hanya in their conversations nowadays. It may sound too formal, poetic, dramatic and classical to some people too. On the other hand, Saja and Cuma is the one to use to sound less awkward in conversations. To help you differentiate the use of them in general, Saja is usually used at the end of a sentence and Cuma is commonly used at the front.
Eg: I only have 1 Ringgit
"Saya ada 1 Ringgit saja"
"Saya cuma ada 1 Ringgit"
Don't worry. You should be able to differentiate them anytime soon now. Try socializing with the natives as those three words are like VERY FREQUENTLY used. It might help you better. Good luck :)