You mentioned "filter", what type of filter are you talking about? Most people would agree that if you are doing a reef tank, you should not have any mechanical filtration media (ie, sponges, bio balls, etc). Your live rock, sand, and skimmer should do the filtration, as well as regular water changes. Algea blooms are a stage a tank will go through as it matures, if your tank is still young, then algea is probably normal and will go away on it's own. I do think that sand is a better decision than crushed coral, but to change it out while there is stuff in the tank is going to be tricky at best! But it sounds like you are going about it the correct way. Just keep an eye on your levels, and get rid of that filter sponge. If you need to get solid material out of your tank, use a siphon and do it during a water change. Good luck.