Err, not sure what you mean by "use the JTAG server". It's there and should just work without special configuration.
If you want to connect applications on one machine to JTAG cables on another (remote JTAG) then you will need to let TCP port 1309 through the firewall on the machine with the JTAG cables attached. Then set a password on the machine with the cables and tell the machine with the applications the name of the other machine and its password.
IE. First, on the machine with the hardware:
1) Open TCP port 1309 on firewall.
2) `jtagconfig --enableremote <password>`
Then, on the machine with the applications:
3) `jtagconfig --addserver <name> <password>`
4) `jtagconfig` (just to check that it worked).
After this it should appear as an option in the GUI dropdown lists as normal. We've run some tests on hardware halfway around the world and everything works OK, but a little slowly.