I already have an ssh agent set up, and I can run commands on an external server in Bash script doing stuff like:
ssh blah_server "ls; pwd;"
I see two ways:
First you make a control socket like this:
ssh -oControlMaster=yes -oControlPath=~/.ssh/ssh-%r-%h-%p
and run your commands
ssh -oControlMaster=no -oControlPath=~/.ssh/ssh-%r-%h-%p -t
This way you can write an ssh command without actually reconnecting to the server.
The second would be to dynamically generate the script, scping it and running.