CONGRATULATIONS!!! All your efforts have paid off!! Smell that...? The sweet smell of success! Ahh... oh so sweet! Your fuge is doing EXACTLY what it is meant to!!
I can't give you exact pruning advice b/c I haven't seen your system personally but I'll just give you an example of mine.
I currently have my chaeto in a 30gal breeder (36" wide, 13" tall, 18" deep). I started with about a softball size wad of Chaeto. Within a month it grows to well over a basketball size and starts to shade the frag portion of my fuge. I then prune it back to softball size.... next month... it's the size of a basketball again and gets pruned back again.
Your chaeto/caulerpa is absorbing the nutrients before unwanted algae (hair, bryopsis, bubble, cyano-bac) has a chance to. It's keeping your tank healthy and clean. When you prune it you are removing excess nutrients that would otherwise fuel unwanted algae growth. So when you prune you should think of it like dumping out a nasty handful of Nitrate, phosphate and heavy metals that would have otherwise remained in your tank and fueled unwanted algae growth.
I know it's tough to prune b/c the chaeto is literally loaded with pods and bristleworms (the stuff we work so hard to get in the beginning

). At first I just threw it out in the backyard but now I either give it away locally, sell it to people for el-cheapo (ie, shipping plus handling) or include it as a 'freebie' whenever I trade or sell frags.
I don't have caulerpa (it scares me

) but I'm sure you could do the same with it. Meet some buddies locally and offer it up for free. You never know when they'll return the favor via coral or help in some way. Heck, ask your LFS if they will take it for store credit... they may not give you much credit for it but heck something's better than nothing..... right? If you could work it out to where your chaeto/caulerpa production supplied you with free salt (or other) then you've just reduced your cost of reefing..... and everybody loves that right?
Congrats again on getting even closer to your degree in 'Reefology'!! Next thing you know you'll be digging mud in the marsh for your turtle grass

. Cheers to the addiction!!
