BIAB has it's own unique notation editor. While it has a number of features, it's really there more as a convenience to the users, as dedicated notation editing is not the purpose of BIAB.
I personally use a separate notation program, and then just export MIDI from my notation program and then import MIDI into BIAB when I want the notes in BIAB. My go to program is Noteworthy Composer (while not as full featured as the big boys, still has a lot of ability and was one of the first that I learned). It costs $49. You can also get MuseScore for free. I also use Notion, Finale, and Sibelius, as the need arises, but they are not free.
That being said, in BIAB, it will honor your key signature, so be sure to set the key of the song before entering notes (so in the key of D, all C's and F's will be sharped). You won't see the sharps on the notes themselves (because they are in the key signature), but the notes are correct. However, if you have true accidentals, you can just right click on the note and use the "Force Accidental" box, where you can choose sharp or flat or natural.
If you haven't, you should read through the section in the user's manual. Just bring up the PDF and search for "Editable Notation".
BIAB has a unique input method where you click on the staff and it enters a very long note. This doesn't mean that your first note is 6 beats long, because all you have to do is enter the next next and it shortens the first not accordingly. If you want to enter a hard rest, just click on the "rest" checkbox and click on the staff and it will again shorten the not that's there and enter a rest. Once you use it a few times, you do get the hang of it, but it's unlike any other notation program.
Here are some links to Notation videos that PGMusic has produced (which unfortunately I did not have time to preview, but will hopefully help and not take up much of your time):
http://youtu.be/Twyl0qNMhBohttp://youtu.be/uIv3fRmhlsQhttp://youtu.be/NolLEQNl_FM