I sort all of the wash transactions to the top of my import file, and sort those wash transactions so the ones with some allowable loss are at the very top. Import, go into the grid at the top, enter your wash sale amounts for the ones with some allowable loss, continue on down with -1 for the ones that are a complete wash.

A billion years ago, when covered transactions weren't a thing, I got to have some input into how the import functionality would work. "You think we need to have a column for wash sales?" "Nah, hardly anyone ever has that many of them, we can probably do without." Ah, foolish Past-Phoebe!