I don't see any entirely satisfactory solution for you.
On the Capital Asset Sales Worksheet, on the first line of each entry, to the right of the description, there is a line that says "Check here if this summarizes multiple sales" and there is a check box to the right of that. When you check that box, the sale will be removed from Form 8949 and added to Schedule D line 1a or 8a as appropriate. But if you have hundreds of sales, going through the worksheets and checking that box for every sale might not be practical.
Perhaps a better approach would be to not import the transactions, or delete the ones you have already imported, and make summary entries manually. When you start to enter sales from a particular brokerage, one of the screens asks you how you want to enter the sales. It gives you a choice of "Sales section totals" or "One by one." If you select "Sales section totals," you just enter the total proceeds and basis from your brokerage statement for each sales section. The ones for which you select "basis reported to IRS" will be added to Schedule D line 1a or 8a and will not be listed on Form 8949.
