You can use your hand controller with EQMOD if you use it in the PC Direct mode which is in Utilities, I think, of your hand controller. You use the cable that came with your EQ6 plugged into the bottom of the hand controller and the other end to a serial port or a USB to Serial adapter. Then use a planetarium to drive the mount.
You can also purchase an EQDIRECT module through Shoestring Astronomy or I think Bintel now have some Shoestring products, and this then goes where the hand controller used to plug into and put the hand controller in the cupboard. You then connect a straight through serial cable to it from your PC or a USB to Serial adapter and use a planetarium to drive the mount.
The third way to do it is to buy an FTDI USB 232 TTL 5 Volt cable from Dontronics, a D9 connector and shell from Jaycar, and make your own cable, taking away the EQDIRECT and providing a higher level of reliability over USB to Serial adapters.
The EQDirect module and the GPUSB are two different animals and should never be tried to be plugged into each other. If you are talking about EQMOD's pulse guiding routine, you just plug the EQDIRECT into the hand controller port of the mount, the other end to a USB to serial adapter or your PC if fitted with a serial port, and enable pulse guiding from the properties menu in the Telescope Chooser when you set up. You do not need to plug in the GPUSB to the auto guider port or the hand controller at all.
EQMOD has a very good Wiki(instruction manual) that should explain most of what you need to know, or you can join their Yahoo tech group for advice and search through old messages that may already have many of the answers to your questions.
PS: I use and old PS2 dual shock controller to drive the mount to the first star if it is off, which you can calibrate and select what buttons you want to use in the EQMOD window that pops up after you get a successful connection to the mount. I then go back to my warm room and use my cameras to line up any further alignment star on my screen with cross hairs and the EQMOD interface.
PPS: Set it up during the day with just the mount on the tripod and all connected to familiarize yourself with its functions before taking it out and getting frustrated at night because it doesn't work.