Sounds like you're using netatalk to transfer roms to your phone. ** Make sure you backup all the roms on your phone before proceeding **
Here's what you need to do (make sure you have bossprefs if you don't already).
1. install OpenSSH from cydia - make sure it's turned on in bossprefs after install
2. download and install Cyberduck for Mac (I believe FileZilla should work fine if you're using a PC)
3. backup your current roms and then remove and recreate your "NES" roms folder on your iphone - this will remove those hidden appledouble file - supposedly it's caused by a permissions glitch with netatalk
4. find out your iphone's IP address on your wifi network
5. start up cyberduck and use that IP address in the server box, also make sure SFTP is the protocol. use 'root' for username and 'alpine' for password.
6. connect and upload your NES roms again!
Oh, and don't forget to remove netatalk after you're done - you don't want your iphone visible on all wifi networks! Also, when you're not uploading files, make sure to turn off OpenSSH in bossprefs.