Adam,
Your base rock will not take long to become populated with bacterium that will aid in the biological filtration. It will take longer, however, to become "live" in the way that most want it to be..meaning, with pods, worms,
coralline algae etc.
You should proceed in your stocking plan just as you would with ANY tank, any configuration of filtration,
live rock etc.... Slowly! Although the rock may be settled in, and your water parameters leveled, the addition of any life form will cause a tiny spike in
ammonia/wastes and therefore a tiny cycle as the chain of required bacteria "catch up". This happens over and over as you add anything that increases the needs of filtration. Check your water often, and when it is settled again, you can add your second specimen. Do this over and over until you meet your stocking goals. Which, I would hope in that tank, are light...for now. Keep in mind that a "clean up crew" will not fare well if there is little to clean up. They would need to be fed as there would be little waste at this point for them to consume. Also, typical "cleaners" are chosen to consume things we despise. Feeding them "prime reef" may turn them off from eating what you had hoped they would. My peppermint shrimp will laugh at aptasia if they get fresh mysid. Make your clean up crew match the needs and add more as you add more corals, fish etc.
Personally, I put new, base rock on the bottom...well...lets start over. I'd add the sand, both dead and live. I would then either use
PVC or some smallish dead, base rock as the "stand" for the
live rock. You really don't want it sitting on the sand (rock could shift and slide and in a small tank with thinnish glass, cause a disaster), but more stable, in contact with the tank bottom.
PVC stands work well. Again, base rock can do the same, but it's a shame to bury rock.
Then, I'd add the true base rock, and the
live rock on top. "Gravity happens", and the
coralline and other goodies on the base rock will fall downward in your system. Sure, bugs and worms and such move where they want, but other "incidental" seeding happens by way of falling downward and landing on the rock below.
Another trick I use, is to find a smallish, golf ball sized of good,
coralline encrusted rock and pulverize it in a towel or something, using a hammer. Take this "dust" and sprinkle it over the rockwork. It will settle into cracks and such and begin to bond and spread. Within a couple of weeks, if you have any rubble that is on the sand and that happens to bother you, pick it out. Eventually, the rock will begin to become covered with algae etc.
I've also seeded
live rock when scraping
coralline off of the glass. Smallish pieces will drift onto rocks and settle. If you scrape a good section, and get small "sheets" of
coralline, you can tuck them into nooks and crannies in the rock.
Also keep in mind that if you have a working
refugium, or a friend with a good, established system, you can get
macro algae or rubble from them to seed your tank with copepods, isopods, amphipods, small collonista snails, astrina stars, micro brittle stars, mysid shrimp and other goodies that will take off like wild fire, in a new, under populated tank.
Don't ever apologize for asking questions... at least not here. That's what we're all about. Talkingreef is NOT like other large boards/communities where egos rule and more experienced hobbyists have little tolerance towards what they feel are "newbie" questions. Your asking, may help another visitor (who may not be confident in posting) get the answers that he/she need to be successful.
Dave
If you use the macro as a transfer vessel, from a 
Linear Mode
