Whats the best way to organize?

I dragged a Jay dee kit folder into my mpc via usb.I loaded the folder and went to main and there was a program named Dilla.I didnt make that program.I thought if i loaded folders with samples into my mpc it would be much easier and quicker than just sample by sample.But when i loaded the jay D folder i thought i could look in the folder at the samples and load and program which samples i wanted.

Make folders in the MPC where your loading to...this way it's exactly where you put it.