rsorbo, if I got your question right you are asking what "CHMOD 666" means, right?
CHMOD 666 is the octal writing of allowing everyone (owner, group, world in Transmit terms) read and write access to that file (or folder).
CHMOD 777 is the octal for allowing everyone everything: read, write, execute (what this means for a folder I think you've to consult a *nix documentation

)
Regarding batch mode Transmit v. 2.1 sort of enables that: select all your files you want to change (all these files have to be in one folder) and hit command-i - a "change permissions" window that is used for all hightlighted files opens.
HTH,
Bernd