Either change both sites to use the same command prefix (set ioBvar(cmdpre) "!") or you'll have to make a few changes to the ioBanana.tcl on both sites.
Search for:
Code:
bind pub - $ioBvar(cmdpre)bw bwalias
Above or below it, add:
Code:
bind pub - !bw bwalias
Then just type !bw in the channel, repeat the process for any other commands.