Thanks for all the input guys.
I was doing what rda990 said, but you either have to overwrite one by one or overwrite all--so if I have two MODIFIED files i'd have to overwrite all just to overwrite those two.. if that makes any sense.
I tried MML and DoubleTwist, and they (as you guys probably already know) only sync certain files.
So, I took takeshi's advice, and downloaded a backup program. I found a nice program called "Alway Sync"
Allway Sync: Free File Synchronization, Backup, Data Replication, PC Sync Software, Freeware, File Sync, Data Synchronization Software
It's an easy to use program. When it opens up, you have one source/drive on the left, and another source/drive on the right.
On the left source/drive, I selected my mounted droid (drive G)
On the right source/drive, I selected a new folder I created on my HDD called DROID SYNC INFO
Then, I clicked "Analyze". It analyzed the two locations and came up with a warning stating that the differences between the two locations were significant, but that was normal if it was my first job. So I clicked "Ignore" and then proceeded to sync.
The sync job was as quick as any other program I have tried. Sync'd ALL files on SD card.
Then upon completion, I closed Alway Sync, unmounted my phone and used my droid to download a pic from the internet and played Snesoid and saved a few save states in one of the games.
I connected my phone back to PC, mounted the card and opened Alway Sync and clicked "Analyze". It indicated that I had one new file and 4 changed files. I clicked "Syncronize" and it copied over the new file and replaced the 4 changed files (save slots from Snesoid).
I haven't explored the other options of Alway Sync (like any auto-sync option or schedule option), but the program seems to have a lot of options. It is free, quick and easy.
Now I can use Astro to backup my apps to the card, and use Alway Sync to backup my SD card to PC without the need to replace files that already exist and have not been modified. In addition, when you open Alway Sync it comes up with the previous two drives/folders used, so in theory all you need to do is mount you phone, open the program and click analyze (or skip and just sync) --no need to find locations again (unless drive G changes for some reason, i.e. different USB port or a thumb drive plugged in)
i've had to use it and it works great