Confirm that it does have the means for those extra ports, as idiotec said.
If it does, and it should, then look at the board and see if you see a couple of like 6 by2 arrays of pins, with a pin missing on a corner, like this,
Those are the connectors for external USB. On your case there should be leads that match up to those arrays. Look in you manual for the pin designations, then look on the connectors on the case leads for pin designations, then match em up. If there is no lettering on the leads from your case, then look at the stuff that came with said case for a sheet of paper with pin designations and match up the colors.
AGP won\'t fit in PCI-E... unless you use a really good hammer. ~Trotter