Bulkheads can be used when running a mini reef filtration system. Excellent system great long term but pricey initial setup.
Regarding the placement of holes, the crucial factor here is the outlet and inlet placement rather than placement of said holes. Inlet should be nearer the bottom of the vivarium outlet nearer the top of the water line, setup to suit personal preference. A cost effective way around it all would be a canister filter running between 600 to 2400 litres per hour (I always prefer over kill so 2400 but most canister filters come with flow control so you can adjust to suit. The most important thing with the canister filter is that it has 3 to 4 media baskets so you get more room for filter wool to clean and things like bio balls to build the benificial bacteria. I usually run two baskets bio balls and 2 baskets filter wool of different grades. Cannister filters on ebay can be as cheap as $50 running up into the $1000 mark which will have built in UV, heater, thermostat and able to analyse all your water parameters.
Now with this basic set up allow to run for 4 weeks with NO WATER CHANGES (spot cleaning out poo is ok
). The bacteria needs this time to establish, flushing large amounts of fresh water will kill of the good bacteria. After this initial period you can change out water at 1/3 capacity every 4 weeks or so. To test water buy a basic ph test kit $20 roughly which checks for ammonia nitrate/nitrite being the most important. I could waffle on for hours so I will stop now. One last thing, the bio balls as mentioned before get rinsed off in the established water once every 3 months to remove gunk but don't rinse in fresh water. Hope this helps a little.