I get a lot of customers wanting to bring me their own shirts. First make sure to let them know in writing that you are not responsible if something happens to a shirt. I had a customer recently tell me that they wanted a shirt with a design like one I had posted on Facebook which had a red fill and a crystal outline. After I made the shirt, which was hers, she told me that she meant she wanted a crystal fill and red outline. Not my fault.
If you provide the shirts, you are only paying a few dollars per shirt, right? So if you mess one up, your costs are limited and you can easily replace it. But if you're using a customer's shirt, they're usually retail and they paid anywhere from $10-$25 for the blank.
Okay, that out of the way, I tell my customers that I take $3 off for them to bring their own shirts. If they balk, I tell them that my price isn't based solely on the cost of materials but on the labor and designing that went into creating that rhinestone transfer. I've never had anyone complain though. If they want to bring in their own shirt, it's because they've found one that they're sure fits them and that they love the way it looks on them. They're usually just thrilled that I'm willing to use their own shirt.