After playing with the project settings for the last few days, I managed to distribute the EAR to both WAS6.1 and WAS7. I can't say for certain what it was precisely that got everything working but I know one main thing was to have the Target Runtime set to both WAS6.1 and WAS7. I did seem to have some problems where some of the projects had been changed to work with WAS7 and didn't show any problems in build targeting both runtimes until I ran it on WAS6.1. Then some annotation problems cropped up when I removed WAS7 as a target runtime. One annotation problem I encountered was that, because WAS6.1 runs on java 1.5, I had errors caused by some @Override annotations on a class which only implemented an interface... so either way I'm glad I found that. Apparently, java 1.6 doesn't care and just lets you override nothing.
Anyway, basically a simply matter of configuring the facets and target runtimes correctly, and making sure that the EAR and sub projects work with each, and not just both.