Ideally, SH3Commander should be installed before any mods are added/enabled. If you are using JSGME just disable them and install SH3Cmdr. I don't know what will happen if Cmdr is installed with active mods. Do so at your own risk.
Changing options in SH3Cmdr while at sea is a big no no. Always make changes while in port and with SH3Cmdr rolled back.
There are certain mods which can be enabled at sea, things like texture files & sounds. However, again, do so at your own risk.
To be safe all mods/SH3Cmdr changes should be made while in port before your next patrol.
You don't want to be back here trying to fix something which broke due to the changes, do you?
