Ways to export as mobile

hi. there is Flash, plus there is Flash builder. Flash has the option to export to mobile air from the same Flash environment. Why are there two tools that apparently do the same, or what is the difference between each one, and are there any other options to create mobile apps from actionscript 3? If so, what is the difference between each option, and advantages or disadvantages?
also, 2. In the documentation about exporting as a mobile air app. they mention something about getting a code or something like that (I remember seeing it somewhere, but right now I can not find the specific document that said it). It said something about getting a code or something like that from an authorized entity. Do I have to do whatever to publish an app made with Flash (or Flash builder), or just tell from the flash environment to export as android air or ios air, then upload in my account. besides that, that should be simple enough and it is what is done if the application was made with any other developing tool?
3. here is the state of my app, currently in development. I took old things I've made in Flash, now I am converting them to actionscript 3, its almost done, but I am using an old Flash (CS3). This was the first flash to support actionscript 3, but is quite buggy. It does not even support 3D, or 3D bitmap manipulation, and even the canvas functions are all messed up, since unlike actionscript 2 with equivalent functions, can not separate correctly the boundary edges of an enclosed region. Anyway, with some tweaks, I've made it work, but there are some things that look like trouble:
In the current version I am using, lets say that I have a movie clip, with export linkage, and that inside that movie clip there is also another named movie clip. So for example, the movie clip in the library is called 'enemy_1', and inside there are movie clips named 'running, dying, quiet etc'. not the real case, but a very close one that many people can relate to. So I've created like a hundred (more than a hundred) of those, and when I am gonna call some_object.appearance.running, some times it gets it correctly, and some times it does not. In all th eprogram there is not aline where I delete a movie clip of these, or change its name, or remove it from its container. I even tried to check the names after creating them, and even so, it gives error sometimes. It started giving me exceptions about trying to access the properties of a null object, because it had not created it correctly. So to avoid things like that, I stopped using movie clips inside movie clips created dynamically, and instead of having a different sprite for each state, I placed all frames in the main time line of the template movie. Not ideal, but it works.
Anyway, there is an option to export to air 1.0 from flash cs3. Not 'android air', or 'ios air', just air 1.0. I tested to export what I have so far to air 1.0 from flash cs3, and even though it was working ok, now it messes up the frames, like it messed the movie clip names before. The exactly same project, that I have tested many times and finally is working fine in the Flash environment, is messing the frames when I tell it to export it for air 1.0, and the sprites show something irrelevant for each case, sometimes (just like with the movie clip names, some times it gets it right, some times it gets it wrong)
as3 was made long ago, and I have a legal license of cs 5.5. I have not installed it yet, because for what I am doing so far, the one I have currently installed works fine (most of the time), but to export it as a mobile application, I plan to install and use the 5.5
Anyway, even though cs3 was made long ago (and it could not get right geometric transformations at the beginning, till a patch was released.. it was quite messed up), I am wondering if after all that time, I should expect more surprises like that before making the mobile apps. Or in other words, what should I expect. I have a nearly finished project that is working fine in as3, made in cs3. I plan to release it as a mobile application. What to do next or what to expect next? I just plan to install cs 5.5, which I expect will be less buggy and will have solved many things I've seen so far in the version I am currently using, and I plan to just load there, and tell it to export as android air, and ios air, and upload in my account. what else do I need? what else is missing? should I look for another path, like Flash builder? what is the difference? is there any other better path?
tnx

Hi,
You might try this:
Make your work area sorta small for this TEST....so you don't have to wait forever to see result...if it works, expand work area to the whole video...
You're going to export the "work area" ...rather than whole sequence...
Use format H.264
choose PAL DV preset
adjust ( in video tab ) frame width and height ( 720x480)
quality 85
make fps same as source
adjust as needed....field order ( lower probably ), aspect ratio ( probably 4:3)
bitrate ( depends on what you're going to use it for ...DVD you can do CBR 8000 kbps I think...2 pass VBR for better quality...have to experiment on this depending on what you use the end product for  ( web, dvd, etc ))
Will make an MP4
Rod

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