We have a league based system currently that we use to play on FAs every weekend... so why not bring a FAs Cup somehow? it would be like the regular cup, just take th teams from the top server in groups of 64 to create a cup group...
So we could have groups of 32 teams starting from 1/16and play 5 cup rounds during the season.
Top 32 would be part of the same tournament, 33-64th secong cup group and so.