Set Alias for Terminal Window in Applescript
What you really need to save are the tabs—those can be used again in a do script action (even if they are just one per window).

This script:


tell application "Terminal"
    activate
    set tab1 to (do script "echo foo")
    do script "echo bar" in tab1
    do script "echo baz" -- in new window
    do script "echo back again" in tab1
end tell


will produce this in one window:

$ echo foo
foo
$ echo bar
bar
$ echo back again
back again
$


and this in another:

$ echo baz
baz