You won't hurt anything leaving a filter in the stock location. I recommend leaving either a stock filter (or better still the CAT filter conversion) on for at least 5,000 miles to purge any debris out of the lines from the lift pump to the stock filter head before removing the filter.
If you install the lift pump and remove the stock filter at the same time, you have about 10' of fuel line full of unfiltered fuel & years of residue on the walls of the line, that will get pushed straight into your CP3!
I ran an AirDog and the stock filter for years before the stock filter head started leaking badly enough I just ripped it out. But until you have a problem with it, I would be inclined to leave it for peace of mind. It won't hurt flow in any meaningful way with the pressure of the lift pump behind it.