Skype's really easy to set up. It's just a way to make two-way audio links between computers like making a phone call.
Download and install.
Make two accounts.
It'll walk you through audio setup, you will have a chance to pick devices if you want to use something like an external USB sound card to interface with the rig audio...
Log in to Skype on the shack computer, and in the options, set it to only accept calls from people on your contact list, and set it to auto-answer.
Add your other account as a contact.
Now you can call yourself over the internet and have your station computer pick up. Skype is full duplex so it'll handle transmit and receive audio. In my case, my radio supports a software command to go into transmit... so I just hit the "TX" button in Ham Radio Deluxe and talk into the computer mic... and I'm transmitting...
I still haven't figured out if you can turn the noise canceller off for the received audio though. So maybe there's a better VOIP solution than current Skype for ham radio remote use... it makes the recieved audio pretty wonky when you're tuning the bands.
Here's some info from someone else who set this up, including instructions on getting a fixed domain name to point to your computer (an important step if, like most people, you're on a cable modem or something else with dynamic IP):http://www.k6br.net/HRD_remote.pdf
But honestly, if you can get the rig control running, you can get the Skype link running. It's the easy part.