First of all, let me say that there's absolutely no need to build your sprite-sheets manually. There are some very good tools for this purpose. Also exporting animations from Flash should be easy and straight-forward. Here's how you do it:
You can export your animations by selecting File
> Export
> Export Movie...
. Then you select PNG Sequence
as format and it will export to a series of PNG files.
Then you can head over to this questionthis question where you'll find lots of good answers on how to create sprite-sheets from these PNGs.
Flash CS6 will have a feature to directly export animations to sprite-sheets. Older versions will have to use the procedure outlined above.