When I need to make a melody I use Sibelius, I used to use Encore. Like you, I find it faster to enter midi info with a real notation program. If you are proficient with Finale that's way to go. As far as 1st and 2nd endings, codas etc... IMHO it's still faster to write it out. Heck all you are doing in a notation program is cut and paste. Once you write out the melody once, you just copy whatever else you need. As far as dumping in into BIAB I believe someone suggested a link to go to. I learned it from trial and error many years ago. I find it simpler just to write the whole song out. When it comes to midi melodies and codas I always end up with something funky happening with my melody. It could be something I'm doing wrong. I usually don't have any problems if I'm just doing repeats. The best way to do that is just write your song as 1 time through, load your melody and then change it to how many choruses you want. BIAB will ask (at least it used to) if you want to copy the melody to match the number of choruses. I hope this helps, I'm far from an expert and I'm sure other BIAB Ninja's are out there with an even better answer than mine.

Dell Studio 16 Laptop i7 with 256 gig SSD
BIAB, Reaper, Encore, Sibelius
Roland SD-50