Well first, have you seen
http://lisimba.org/minecraft/howto_beginner_reactor/howto.html ? It's an awesome guide which I've used to build mine, has some notes on efficiency as well.
Two things I've discovered, personally, though:
1. You don't need much CO2. If you're using RoC pipes, 2-3 buckets per pipe segment, no more, otherwise it'll jam up at the heat exchanger. For automation of CO2 production, just pipe charcoal+logs into the furnace, loop it back onto itself so it uses the charcoal it creates, and make a pipe from the top of the collector to your storage medium.
2. It may have been fixed in later versions but in Monster 1.1.2, Ammonia isn't usable - it goes into the steam boilers, heats up, and.....vanishes.
Here's my current setup, nothing big:
It's a relatively simple 4-core with a closed-CO2 loop, goes to heat exchanger with 3 steam boilers attached. Generates enough steam in a snow biome to run two turbines. I plan to use it to power the infrastructure for my fusion reactor (under construction, located outside), currently it just runs the extractor and a couple mining lasers. Fuel is autocrafted on demand in the first basement and supplied via the LPs, waste goes into the ME system in the background. The blocks around the boilers are actually unnecessary, but it looks cleaner with them there IMO.