Well, you could theoretically make a new ant run config that runs the debug-deploy target, and a new remote debug configuration that connects to the remote jvm session. I haven't tried it, but I just went and looked at the plugin source, and I think these are the parameters you'll need to set:
Connection Type: Standard (Socket Attach)
Host: <YOUR IP HERE>
Port: 8348
No guarantees that these are the actual correct parameters, as I didn't write any part of the plugin, but if I'm reading it correctly, then that's what you're looking for. If you're interested in taking a look yourself (if that doesn't work), then visit
https://usfirst.collab.net/sf/projects/wpilib/ and follow the instructions to look at the source. The particular file I'm pulling this info from is eclipse-plugins/<long package name>.java/src/main/java/<more packages>/launching/JavaLaunchShortcut.java, in the getRemoteDebugConfig method. Hope that helps.