Click “+ Custom Contest” on the “Contests” page, fill in the contest's details, and save it.
You'll need a name, field lineups, and the payout structure. The payout structure can either use the structure from an existing contest, or be customized by manually setting the number of entries, the % to first, and the % of the field that cashes.
User Entries determines how many of your lineups exist in the contest sim. Having this number set higher will mean that the results of the contest sim are more heavily diversified, to avoid a situation where you lineups cannibalize the EV of other lineups you play.
For Field Lineups, choose the stakes bucket closest to the entry fee: Low Stakes is $4 and under, Flagship is $4.01 to $30, Med Stakes is $30.01 to $99.99, and High Stakes is $100 and up.
Custom contests are for anything that doesn't come through your entries file: private leagues, unusual formats, or a contest you want to test before entering it. They run with the same game simulations and field lineups as everything else, so the Sim ROI you get back means the same thing.