Most mods, including the STM all have files such as Installation or Read-Me that give you vital information.
The reason the files are not posted as self extracting programs is because I got a lot of emails from people telling me they will not run such a program. (Fears of virus and such.)
So if you read the installation text that came with the Star Trek mod you will find that it has answers to many issues.
I hope the ST mod is working well for you and that you enjoy playing it.