Is there any downside covering my substrate with pea gravel? Or is it better to mix it ? Will it still suck up the goodies (crap) from the fishies?

I have a 55 gallon aquarium with a substrate consisting of approximately 1” of sand covered by 2” of pea gravel from Lowe’s. 2 watts/gal fluorescent lights and a DIY CO2 system (yeast, sugar) plus all the usual equipment/maintenance (filter, heater, air and water pump, weekly vacuum and water...