In my case, the server offers IMAP and both clients use IMAP (or at least, Microsoft's proprietary implementation of something that looks like IMAP), so there is little interaction between them. I have both Thunderbird and Outlook on my work computer. On the rare occasions where I run Outlook (usually out of desperation, to work with a shared calendar), I find that regardless of my settings, Outlook always configures itself as the default mail client, and so next time I run Thunderbird I have to reassure it that it is my preferred client. A mix of POP on one and IMAP on the other is unlikely to work well.
If you have been using Outlook for a number of years, there is a distinct possibility of it using POP. This isn't a concern if you use IMAP, since both clients would be looking at the same set of folders on the IMAP server. You'll need to set both clients to leave copies on the server. If you use POP, then there will, by default, be a "first come first served" process, whereby your messages will be collected by whichever client runs first. But you'll need to think about how and where your messages are saved.
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