If your mini-USB adapter has the DTR signal broke out then just wire it to the reset pin via a series .1ufd capacitor and the Arduino should be able to auto-reset the board prior to uploading a new sketch. If you don't have a means to auto-reset then you have to use the manual reset switch, but the timing of that reset is tricky as there is a pretty short 'window' of when it will work properly with the IDE timing. Most hold the reset button down and release it as soon as the IDE displays the size of the compiled sketch, but again it can be tricky getting it right.