Breaking up large modularity classes

[griffex]

So in a few graphs I run lately I'm finding that I'll end up with a couple very large clusters when I run modularity (3,000+ members), with about 10-12 smaller ones (around 1-200 members). I'm curious if there's an easy way to run modularity again just within those larger clusters to see how their members create clusters within clusters.

The best I've thought so far is to just run each group independently then append them all together afterwards, but I'm worried that could end up looking messy and that the class systems won't carry over.