Side by side would be impratical if one was to be used as a sump.
You would want to place one under the other. Even this could be problematic due to the lower/sump tank needing to house all your hardware. On most occasions the lower tank is smaller LxW wise so when you hang a skimmer on the side, have plugs ans switches etc... all still fits neatly in the cabinet/stand. Now if you were to build an oversize stand for your tank, then you would have the space. Also, building your own stand will allow you to make it a little taller than standard which is a boon because it will be easier to work on your sump and such.
On the plumbing. A drilled tank is the best way to go. You should consider taking the tank to a glass shop and having a hole or two put in it. This will give you the most trouble free method. We can extrapolate further on this if you decide to go this way.
The other way to go is to use an overflow box on the back of the tank. IT siphons water out and sends it below. The rub here is, by the time you buy the box abd an auqualifter to make it as trouble free as possible, you will probably have a larger investment the drilling it in the first place, and it won't be as trouble free.
GL
