For the 1065 there is no checkbox to state whether or not it is a qualified trade or business. An adjusting entry would have to be made. In the Partnership return from the Open Forms menu (F6), type 199a to select the Section 199A Activity Worksheet. In the 199a Activity Worksheet, line 1b you would be able to enter the amount that needs to be adjusted. I know that an enhancement has been entered in hopes that this will be added to a future update of ProSeries.