Matt7, sounds like you are going through some of the same things I have--I am in the process of setting up a 90 gallon system. I have had it for 4 months now, and just added water--no salt yet, just water.
There are multiple "right" ways to do things, and there are some definite wrong ways to do things (adding an anemone to your tank as soon as it cycles, big fish in a small tank, cutting the eurobrace off your tank because it gets in the way of the lights, etc.).
With regard to what order do you add things, here is what I am planning. As soon as I get some of my plumbing worked out I will be on step 3:
1. Pay Reef Central membership so I can use the search feature unhindered
2. Tank, good skimmer, good in-tank flow, empty fuge.
3. Add live rock, 1-2" substrate in main tank, begin feeding tank
4. Add DSB in a bucket
5. Wait for cycle
6. Add clean up crew
7. Start quarantine tank
8. Establish fuge, add 1-2 fish
9. Upgrade lighting to T5s, add auto top-off
10. Start adding corals
11. Let >6 months pass from initial tank cycle
12. Add anemone
13. Wait a couple months
14. Add clownfish
15. At some point, add calc reactor and multi-controller
This certainly isn't the only way to go about it, but I am hoping that it is one of the "right" ways.