Hi Ian,
My understanding is that you cannot separate EPGP for multiple raid groups.
Our guild for example, has two raid groups running and we all have to share the same EPGP system. Suggestions to make it simpler. Have one group awarding more EP so that the raiders from each group tend to separate themselves into layers for PR purposes. This part isn't necessary, but it keeps it cleaner visually since all raiders for a certain group tend to end up lumped next to each other. As well, ensure only one person is doing decay to avoid duping it. And of course, you need to manage any raiders that are running in more than one raid group to ensure they aren't getting extra EP ( Just make sure you detach their main from their alts in the g note ).
We've been running with two groups since December and no problems. Cheers and GL!