It sounds like you like using Manga Studio. You should use whatever you feel comfortable using. As far as inexpensive graphics software goes, I used to use Paint Shop Pro before they went it made it work like Photoshop, essentially ruining it. I have never heard of Manga, but that is probably because I do not do a lot of graphics work these days that requires me to go beyond the tools I have. I have relied on Flash for a lot of the graphics work that I have done over the years. I got used to how it works and made the best of it. If I needed some other software to get the effect I need then that is where I went for it.
When you join/cross lines in flash you create new segments. Your 3 line drawing of a letter A will convert into 5 segments if the lines are all on the same layer and properly connected. There is nothing wrong with that. If you wish to retain the three then you can opt to use different layers for them or draw them each as objects.
When you select the paint bucket there is an extra icon that appears in the palette. It's a circle, and the help tip says "gap size". You can use that the get Flash to fill areas that have gaps in the outline.
Thanks a lot, I agree with you, the segment works great, just one click and I can remove a segment.