I recently upgraded from a paintball co2 setup to a 20 pound canister and full size regulator, and my only regret is I didn't do it sooner. I used my paintball setup on a 75 gallon high-tech setup for about 3 years, and would have to refill the canister once a week, and if the store didn't have any co2 I would have to drive 20 miles one-way to the next store that could fill canisters. There are two main factors, for me at least, when it comes to deciding which route to go:
Price
How long it lasts.
As for price, a full size regulator and bigger canister will cost you a little more up front. A 20 pounds co2 canister around me is $80, used off craigslist there is no need to buy one of these new, and then $20 to exchange it for a filled one. Why? Well there are several reasons why. Mainly because 9 out of 10 places are simply going to exchange your canister for one of their's that is already full. Yes, yes, some people will say "Well Jim-Bob at my local shop will fill it up for me while I wait", you can look for your own Jim-Bob but most places don't refill, hence most. So don't waste your money on a shiny new co2 canister, buy a rusted POS on craigslist and exchange it at the store, if you don't like the way the one you get looks, paint it, or make a sleeve for it out of cloth.
A full size canister also saves you money, on refills and testing. On average a store is charging around $4.50 to refill a 20oz paintball canister, if you do the math you will end up spending $72 on 20 pounds of co2 and making and having to make 16 different trips to the store to refill them, or you could spend $30 for each 20oz canister and get a couple, but to get 20 pounds worth of 20oz canisters would easily cost $480 plus tax, then you have to worry about the hydrostatic dating which you will have to pay to have done for each paintball canister or replace it, this is already taken care of for you when you get a canister at an exchange, you will always get a canister that is full, within the hydrostatic date, and functions properly. AND to me the best part of the exchange is the quickness of it, most places when they see you walking in with a co2 canister over your shoulder they know what you are there for instantly and you will be in and out way faster than having to talk with Jim-Bob while he refills your canister and listen to him tell you about how his wife can't cook and theres no grass growing in his yard this year.
How long will it last? Many people ask this and it varies, it all depends on several things that are hard to judge. Simple things like the amount of flow in your water, where your diffuser is placed, or if its inline, where you drop checker is placed, what kind of test fluid you have in it, if you are using a solenoid or not, and so one and so on. Will all effect how long your co2 lasts. The main thing to take in to account is how are you going to monitor how much co2 you have? The most common way is to use a drop checker, although it is not the most accurate way to check you co2 levels it is affordable. The other key factor to determining how long your co2 canister will last is if you are using a solenoid or not, a solenoid will help you maintain the same amount of co2 flow daily, or you can simply leave your co2 on 24/7. Usually a 20oz canister would last me 5-7 days on my 75 gallon when I was using the paintball setup for it, but on my 10 gallon, the same paintball setup has lasting almost two month so far. I simply got tired of going to the store and having to fill up my canister every week and then I figured out how much I would save by going full size so thats when I swapped over.
I would suggest you start out with the full size regulator and a 10 or 20 pound canister, the main reason I suggest this is because if your aquariums are close enough, or if you don't mind having some tubing running to the other aquarium, which can be done several ways, the easiest way of course is simply letting it sit on top of your floor, the best looking usually is run underneath your flooring like the cable is for your TV this is pretty easy if you have a crawl space, another way you can do it in an apartment if you have a baseboard is take a screwdriver and stuff it under the baseboard the carpet will help hold in in place I do this throughout my entire apartment with cat5 cables, you can easily run both of your setups off of one co2 canister and one regulator. You would just need to get a regulator that either already comes setup for multi-tank use or you can buy a manifold and add it yourself, I have seen some that will run 6 separate aquariums all with independent bubble counters and needle valves.
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