Terminology:
Padded Pogo : the results of testing show that a Pogoshell ROM needs to be padded to the nearest 32kb in order to function with the GB Bridge; this term refers to a Pogoshell ROM that has been padded
GBC games : The total size of all the GBC games you wish to flash
Compilation : The combination of a Padded Pogo and GBC games
loader : GBC2GBA.GB, the preboot file Visoly distributed with Flash Advance Writer 3.2

Here we go:

First off, using Pogoshell & GBBridge on cards lower than 256mb is far more simple than on a 256mb card

*64 mbit card : seems to be not possible due to loader's expected location & PogoShell's handling of these smaller cards
*128 mbit card : Compilation must be less than or equal to 16,744,448 bytes

On a 256mb card, there are two possible methods for using Pogoshell & GBBridge:

1) Compilation is less than or equal to 16,744,448 bytes
2) Compilation is greater than 16,777,216 bytes and Padded Pogo is less than or equal to 16,744,448 bytes

Explanation:
The 256mb card is seen as two 128mb cards. Therefore, if Compilation goes over 128mbit, it must be split between the two "cards".
This is accomplished by placing the loader in the final 32kb of the first 128mbit (beginning at 0xff8000), and having GBC games begin at the beginning of the second 128mbit.
Therefore, if your Padded Pogo is greater than 16,744,448 bytes, there is no room for the loader before moving the GBC games to the second 128mbit section, and therefore is not possible to flash.

Alternate Loader Possibilities
It is possible, since all combinations use a loader placed in the final 32kb of the first 128mbit of space.

Compiling On Your Own:
An automated tool would have to do the following:
1) Create a Pogoshell ROM (e.g. - create.bat)
2) Pad the Pogoshell ROM to the nearest 32kb
3) Compile all wanted GBC roms into one file
4) Check what the size of Step 2 + Step 3 is
5) Follow the above-mentioned procedure for determining how to pad before loader is placed
6a) If Compilation is greater than 16,777,216 bytes, pad the Pogoshell ROM to 16,744,448, and add the loader and GBC games .  
6b) If Compilation is less than or equal to 16,744,448 bytes, combine Step 2 + Step 3 and add loader to final 32kb of file
7) Flash the resulting combined file using whatever program you wish

Please note that this description only created a fully usable Compilation that can be created and flashed by means other than Flash Advance Writer.  This procedure does not alter how saves are handled, but can possibly be used during the compiling to sort the GBC roms in such a way that they will utilize the 64kb of save bank 1 in the most effective manner.

I hope this did not go over everyone's head, but like i said at the beginning, I believe this is the most detailed report of exactly how the GBBridge functions in relation to a flash cartridge.