Re: water separator
According to the instructions that came with my Racor fuel/water separator it could be mounted either upstream or downstream of fuel pumps.
It stated that it's preferred to have the filter/separator upstream of the pump for a couple of reasons. 1) A pump might emulsify any entrained water making it less likely for water to fall to the bottom of the separator bowl. 2) Any crud coming through the line might damage the pump, having the filter/separator before the pump will help prevent that. 3) IF the filter/separator is mounted after a fuel pump you must make sure that the pump can't exceed the maximum pressure rating of the filter.
As far as whether a primer bulb is before or after the filter/separator, it doesn't matter. Water is not going to be sucked through the unit, water falls to the bottom and the outlet is at the top (except as mentioned above where a pump is churning water into tiny droplets and turning the fuel/water mixture into an emulsion - a primer bulb certainly isn't capable of that).