If you want to select multiple files from the file selector dialog that displays when you select browse then you are mostly out of luck. You will need to use a Java applet or something similar (I think there is one that use a small flash file, I will update if I find it). Currently a single file input only allows the selection of a single file.
If you are talking about using multiple file inputs then there shouldn't be much difference from using one. Post some code and I will try to help further.
Update: There is one method to use a single 'browse' button that uses flash. I have never personally used this but I have read a fair amount about it. I think its your best shot.