(Dad here)
This thread brings a lot of questions to mind.
1. I'm confused about the filter sock approach. My understanding is that the Skimmer's sole purpose is to generate bubbles so as to collect waste. So what would be the purpose of trying to remove bubbles before the skimmer?
The skimmer creates bubbles internally. The proteins in the water (mainly poop and uneaten food) stick to those bubbles creating a foam head. The foam head then bubbles over the top of the skimmer into the cup producing the skimate (the bad stuff). You don't want bubbles coming in externally. The filter sock helps reduce or eliminate those external bubbles.
2. As to our skimmer, we've been trying not to spend a lot of money since I've been out of work for while. The one we bought was basically the cheapest 300GPH one on ebay. A no-name brand with a model number of 23PUM003-1802 (see
http://www.thelashop.com/300gph-aquarium-protein-skimmer-filter-pump-fish-tank-powerhead.html). However it still isn't collecting very much, our LFS said not to worry as our tank is new and it likely won't start collecting until we get more fish/bio matter collecting. Still, we're suspicious that we're going to have to replace it anyway...
As you mentioned, when your bio load increases you may want to invest in a better skimmer. It is probably the most important piece of equipment in your system for maintaining a healthy tank. Test for nitrates. If your nitrates are above 5 - 10 ppm, you may want to look into a better skimmer.
3. We currently have algae in our refugium (we have the lighting on an opposite schedule from the tank to help with PH) and have been planning to get some shrimp to live in it as extra food for our tank. That's why the sand and the rock. Currently our flow through the refuge is too high, but I've got some ideas as how to create a bypass so as to slow it down. We're actually thinking of getting some shrimp today to put into it.
Your thinking is right on line - you don't want real high flow through your fuge so that beneficial bacteria and copepods can grow and provide natural filtration and food. Do you mean you have macro-algae (like chaeto) in your fuge? If so, this is also right in line. It eats nitrates and provides a habitat for copepods...
4. As per this thread we've removed the filter from the inside of our return pump. It seems to make things a little better but I'm worried that a piece of algae will make it out of our refugium and get stuck in the pump and break it.
If it didn't solve the problem completely, it may not have been the culprit. As mentioned above, raise your water level in the return section of your sump and see if that helps...
Sorry if I've diverted this thread too much. Let us know if we should branch to new threads.
Don't be sorry - that's what these threads are for...ask any and all questions that you have...
Thanks!
-Mike & Jade