This is what I did to settle on how I stage my tables. I kept buying many different used stages and head amps after I decided on the cartridges I wanted to use. I always had more than one at a time so I could side by side over time and what I liked best stayed. Also just because a phono stage is built into another unit like a preamp doesn't mean a stand alone will be better.
Take your time and listen over days and go back and forth with different music and records. Acclimate to the sounds and or difference your hearing in both stages and a combination with the head amp in the mix.
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You can still use the head amp in conjunction with a stand alone RIAA phono stage, just like you did with the built in RIAA stage in the
Prologue 3. Your head amp most likely has a couple gain setting as dose the project. You also can use the head amp into a MC setting on the project, not just the MM setting. You can play with loading of each and gain to see what combination works well for you.
With these two units together there is no reason to have a low volume input of your cartridge/table. It can be equal and or surpass any other line level input you have, so much so you can push it into distortion. But you can also play your records louder than say a CDP or digital source. Digital and Records are mastered and EQed differently. With digital in my system the speakers can start distorting far far sooner than with a record playing just because of the loudness/bass boost inherent in digital. I can put a record on and just keep going up in SPL and not have distortion stopping me and my system for over all performance output.