You can use the same thru-hull but will need to install line check valves to each discharge line prior to their becoming common discharge. With two electric pumps plumbed this way they would tend to fight each other, with one or the other doing the only work, but with your manual, positive displacement, pump you will not have that problem.
34's idea is the best way to cover all contingencies. I have seen "portable" pumps made up with a small dc pump mounted to a broom handle or such, with the discharge hose running up along the handle, and the electric cord extra long with alligator clips. This allows one to move about, from compartment to compartment, with the pump and not be constrained by discharge plumbing and "hard" electrical wiring.
A strainer box around the base of the pump is not a bad idea, but can probably be omitted if the pump location is readily accessible. "Readily accessible" is usually not the low point in your bilge, unfortunately. It does not hurt to think about having to remove the pump, to clean the suction screen, while having a foot or more of dirty water over it-in the dark! A pump location that may not pump your bilge completely dry, but is easily accessed, may be of more importance when that bad day arrives where you've really got to move some water. Which I guess brings us back to where 34 came in.