q1. when filling the make up tank, when do I add the salt?
If you are topping off the main tank to make up water from the evaporation, you never add salt. Only fresh water evaporates, leaving the tank a little more salty. I would topoff the tank each day if possible to keep fluctuations to a minimum.
q2. how long before the change should I fill the tank?
If you are doing water changes, mix up the salt about 2 days ahead of time and make certain its well dissolved (powerheads hanging in the bucket work well). To fill with RO water timing is not too critical, although I would not leave it sitting with no current for more than a week or two.
q3. a suggestion of turning on the pump in the make up tank to move the water, however, no suggestions of how long to do so. how/when do you make up your water?
Total dissolution usually occurs overnight if you are using a powerhead/pump.
q4. there is a thick smelly ugly algae that fills my overflow slots, grows and hangs all the way down the overflow box, grows over the power heads, and comes out/off easily in large clumps. I cleaned out a large amount from the overflow, and above the power heads, but I did leave some because, it hasn't hurt it yet! is this normal/acceptable and out of control?
It is just hair algae. Its controllable mechanically (using RO water, frequent water changes, and a good skimmer, and pulling it out by hand) or biologically... various fish, hermits, snails will eat it. Keep up with pulling it out or you will find yourself too far behind on it.
q5. when cleaning the algae off the glass I felt that I was sending an awful amount of what seemed to be dust, and algae specks all around the tank. is there a way to get it off without putting it every where?
Not really, although you can use a powerfilter (like a canister filter) to help keep the water polished while you mess around in the tank.
q6. I felt that every time I touched something it felt very fragile. are they this fragile or was I being neurotic?
Depends on what it was, but for hard corals, they frequently are very fragile. As for most things though, they can recover quickly from mild damage. I wouldn't worry about it.
q7. is the hard purple stuff algae anyway?
Corraline algae. Yes, although its a more desirable type (mainly because it looks better).
q9. if I want to move the rocks out of the tank clean the gravel, and put all the rocks back in a completely new arrangement. what should I do with the rocks/animals?
Do not do this unless you plan on re-arranging. If the tank has crushed coral (very course gravelly bits of shell) in it... then I would consider replacing it with araganite sand slowly. If you do it, you should find containers large enough to hold all of the rock and critters for a few days. Use a powerhead for water movement (shield it to protect your fish/inverts from getting sucked in) and if you have corals in the bin, place your lights over it for the time it is being held.
q10. should I even remove them?
If you are removing the crushed coral, then yes. You will stir up alot of junk.
q11. How much water should I remove?
If you can make more RO water, then all of it. Just match the salinity (1.026 or 35 ppt) to the holding tanks. If not, then as much as you can realistically make again when done.
q12. Should I ever reuse the old water?
No. Unless you just can't make enough new water at once.
q13. If you empty a reef tank, clean all animals, rocks, sand, and all equipment with the water taken from the tank, then fill the tank with completely new water, is it the same as starting over?
Not at all. The important part is in and on the live rock and sand. All of the bacteria you need in the tank will still be present. BUT, make certain you match salinity and temperature with the new water... and acclimate your fish and mobile inverts to the new tank water just prior to the change.