On entering ETP and ETE you'd select "This partnership ended..." and then "Disposition was not via a sale". This will allow you to enter the K-1 as you normally would, but will leave the passive losses suspended.
As for merging, the simplest way is to wait until next year. When you're completing the K-1 for ET (or for ETP since its still broken out by ET) you'll get to the question about suspended losses from last year. Edit this entry to be the sum of whatever TT automatically brought over, and what you need to merge.
Note that next year TT will import ETP and ETE again, but you can delete those entries once you've grabbed the suspended losses from them.
One other option, that works only for ETP: ETP continues to exist, and is broken out by ET, so you'll still have an ETP K-1 in TT. If the FEIN hasn't changed, you could simply add the values supplied by ETP (on your final K-1) and by ET (for the ETP sub-K-1) together, and keep processing ETP as normal.