1. You should have an income distribution deduction on Line 18 of your 1041. If you don't and have passed through the gain properly then there might be some sort of issue with the software. Note that the gain must be allocated to income and also to the beneficiaries, and then actually distributed, before the IDD will kick in.
2. I'm not certain about the mechanics of the software but it should allow you to allocate the gain from the sale of part of the trust's holdings to just the three beneficiaries who are receiving cash from the sale. You should be able to do this either by allocating the appropriate percentages or dollar amounts to the beneficiaries who are receiving their share of the gain, and you should be able to exclude yourself or allocate 0 (percent or dollars) to yourself.
