I'm assuming you mean Pro Tools LE- the cheaper version. The answer for the expensive version is something like "spend a lot of money to get all the inputs and outouts you need."
With LE your choices are more limited, but less expensive.
So- assuming you have a 002 or 002r, my first thought is to use the ADAT as extra convertors for the lightpipe I/O on the 002. Yippie- 8 tracks out of 24....
Second thought is to use the ADAT 24 for live tracking and dump the tracks digitally to Pro Tools for editing. With LE you can only do that 8 tracks at a time via the lightpipe, though the ADAT might have a facility to directly transfer its files to your computer- I don't know. At any rate, this is probably the most common way to use a standalone machine in conjunction with a DAW- makes use of the strenths of both.
Take care,
Chris