Most certainly you can use Thunderbird with Tor on Linux. First things
first, unless you want to use Tor only when you open the browser bundle,
which is a safe configuration but not one that is necessary for the use
of Tor with other programs, you need to see whether your distribution
has tor available in the repositories utilized. On the other hand, you
could also load the browser bundle, which will start up Tor, and then
close the browser if you wanted to do so, leaving Tor itself still
running. In any case, you need to look at the Tor settings to see which
port it is utilizing as the Socks proxy. It is likely port #9050, but
check to be sure. Also, check to make sure which address Tor is using
for localhost, which is probably 127.0.0.1, but it could be something else.
Once you know those things, you would need to set up Thunderbird with an
account pointing toward those settings, namely, 127.0.0.1 and port 9050.
There are several other settings that would have to be made, but first
check this much of it out, and then we can go from there.
In addition, you should take a look at
https://trac.torproject.org/projects/tor/wiki/doc/TorifyHOWTO/EMail/Thunderbird