PSFB brings up a good point. Bubble merging can occur if the column is too large or if you inject too much air into it. P.R. Escobals Aquatic System Engineering book has all of the formulas you need to calculate the optimum parameters.
This website is also very helpful.
http://www.hawkfish.org/snailman/skimmer101.htm
Some collection stations and wholesalers use less efficient, oversized skimmers so they can have an impressive picture for their website. Giant phallic symbols don't do much for me, but it lets everybody know "Hey, we may not know what we're doing, but we mean business". It's also easy to talk an investor into something impressive like that, rather than a series of right-sized 6' x 12" skimmers.
A long dwell/contact time is ideal, but there is a limit to contact chamber size. A series of medium to large skimmers will work better than a single oversized unit due to bubble popping and premature merging. It is also more cost effective to use smaller diameter pipe. You can build ten medium sized skimmers for the price of one large one.
Minor changes in salinity (as experienced with large vats in commercial facilities) water level, and air injection, may cease skimmer production. If the skimmer isn't overflowing, it serves no purpose. Multiple skimmers will assure that you aren't putting all of your eggs in one giant, phallic, basket.
Protein skimming is more of a matter of quality than quantity. You should research some of the air-driven skimmer threads here on RC. Plumb the skimmer directly into the overflow and have the water flow to each skimmer in succession.
Protein skimming is difficult with such a high bioload, as experienced with newly acquired live rock. If your plan is to cure live rock on an ongoing basis, then you may be better off focusing your resources in other directions. Biological filtration will remove ammonia and nitrite, which are your main concerns. Nitrate is a non-issue while stabilizing rock. The rock has all the bacteria you need to keep it clean, you just have to harness the power. A stable bacterial colony will break down the die-off occurring around it. Oxygenating the rock & water will solve most of your problem.
I would set-up an ebb & flow system, whereby the vat fills with water, then drains via timer or float switch. The ebb & flow process should take a few minutes and cycle continually. High and low mercury switches will govern the water levels, and back-siphon/gravity (back through the pump to the sump) will drain it. You should plumb in an emergency overflow as a fail-safe.
Alternatively, you could have this set-up to cycle water back and forth between two or more vats. As one fills, the other drains, then reversed. An ebb & flow system will turn your rock into a giant biowheel-style filter. The well oxygenated rock will quickly restore bacterial film and reduce rotting sponges and other casualties. Some oscillating fans will help as well.
Your going to have to set-up something for the smell. Small containers of silica gel can be soaked periodically with liquid air freshener. You could also make a carbon filter out of a 5 gallon bucket and an exhaust fan. Ionizers aren't strong enough to get the job done. An exhaust fan is a good idea though.
Another option is to use ozone with your skimmer. The residual ozone will kill airborne odours as well, but be very careful of exposure to ozone. If dosed properly, the amount of ozone you generate will dissipate as it oxidizes water and airborne organics. If you overdose, you will have residual ozone issues to contend with. The carbon filter will aid in this. You could have the ozonizer on a timer, so it kicks in at night when you're not around. Good ventilation is very important.
