Bilge-pump caveats
By way of example, on Cherubini 44s we fit three bilge pumps-- a Whale or Edson dual-diaphragm manual pump, worth about 30 GPM, and two 1500-2000-GPH pumps stacked one on top of the other in the 'well' (deepest sump of bilge). All three have individual through-hulls in the waterline stripe with seacocks.
The two in the well are a primary dewatering pump and its backup. An indicator light on the panel tells when the secondary pump (the one on top) kicks on. This means one of two things: either your primary pump has failed, so the second one is now working, which means you have about 9" of water in the sump (it's about 32" deep and about 11" x 16" in area); or you are taking on so much water that both pumps have to be running. About 99 percent of the time the light comes on, it will mean the lower pump or its float switch has failed. These boats just don't take on that kind of water volume (seriously, they don't).
If you are fitting a secondary bilge pump, consider making it a backup to the other one. This could mean mounting it slightly higher in elevation, either near to the primary one or else somewhere else in the contiguous bilge system. If you have two separate sumps (not connected except over the floorboards) the two pumps won't serve as backups to each other. The Hunter 25.5 has this problem. I worked on a 1959 Swiftsure that did too. I consider this a major oversight.
Some caveats:
As others have said, absolutely make each pump have a separate exit leading as directly from the pump to the sea as possible. On the C44 we loop each hose up as high as we can, fitted with a vented loop and leading down again to the waterline; this is primarily for aesthetics as they could easily exit right under the gunwale and do without the vented loops. Otherwise every pump-our exit near the waterline must have a vented loop mounted as high as possible, to avoid allowing seawater to siphon back into the bilge (same as with a toilet inlet). Technically check-valves are acceptable as an alternative; in practice, however, they restrict flow where you need it most: between the pump and the through-hull.
On Diana I mounted my (manual and electric) pumps' vented loops inside the cockpit coaming, from underneath. From these aft there is a clean straight downward run to the transom. Outbound from the vented loop, have no uphill turns at all.
Dumping bilge pumps into the cockpit, to save either appearances or installation hassles, is about the worst case of false economy I can think of. All I say to this is: what if the cockpit drain through-hull (typically the biggest through-hull in the boat) is the thing that's leaking? All your bilgewater intake will just be recycled. (Duhh!)
I don't go in for that '6 inches above the waterline' myth. I say ALL through-hulls below the maximum-heel-angle's waterline (more like 6 inches from the gunwale) MUST be fitted with seacocks. (Read cockpit-drain point, above.) This includes those in the transom or stern being above the highest waterline when the boat is poorly loaded (such as with seawater in the cockpit), riding big sea or surfing/surging. All these fittings should be double-clamped and should use heavy-duty PVC seawater/sanitation hose (Shields 148 or Trident equivalent). I would recommend Marelon ones for the seacocks, especially if they are located where you find it awkward to lubricate zerk fittings every month for the rest of your life.
That brings us to: all seacocks should be readily accessible, not restricted by fittings, bulkheads, stowed gear or gymnastic requirements from being turned easily and regularly. Bilge-pump outlets mounted in the rear quarters of the boat can be the worst culprits for this.
If you have to mount a bilge pump rather far forward, there is nothing wrong with having it exit the side of the boat. Just fit the vented loop and seacock appropriately (both being all the more important the farther forward they are located).
Lastly: the less hose the better. A direct route, with no pipe elbows and extra hose clamps, is always preferable. If the pump has to be rather far forward this is one major point in favor of its exit being amidships.
