Umm no the packets or IVs won't be saved there unless you explicitly specify. If you change directories into the SD card then it will save the files there. Alternatively you can specify the absolute path:
# airodump-ng wlan0 -w /media/mmc1/mycapture --ivs

Also I might mention (although should be irrelevant if you are using the internal wifi card) that if you use an ARP attack (aireplay-ng -3) you need to be CD'd into the directory you want the replay .cap files to be saved.

It seems like you need to visit some general linux forums and brush up on the basics. Additionally the backtrack forums might help for the aircrack suite specific stuff. (Especially since discussion of these topics is frowned upon on this forum *rolls eyes*)