You can run multiple instances of Thunderbird with different user profiles for each instance, by launching it from command line as:
[marios@bate ~]$ thunderbird -no-remote -P work & [marios@bate ~]$ thunderbird -no-remote -P personal &
The -P option defines the profile name. If you want to create a new profile, use -P without a name.
NOTE: This article is a short version of Run multiple copies of Thunderbird at the same time from the Mozilla Knowledge Base.