First
BACK UP what you have, just in case something goes wrong (and it could, simply because the version you are using is very old).
You may want to join the mail list. See
http://www.os2voice.org/mailinglists.html. That is the best place to ask questions, and find answers to problems, but you need a working mail program to use it.
Next, be sure to READ the information that is presented by the installer, and it would probably be a good idea to look through the FAQ
http://pmmail.os2voice.org/index.php?title=PMMail_FAQ. Setting up secure server support is explained in the FAQ, in a different way than it is in the Help. Some people find one, or the other, to be confusing, but they usually figure it out by using both.
I would suggest that you think about reducing the number of messages in the primary folders (Inbox, Sent, and any that you filter messages to). I usually put old messages into sub folders, by year, or month, depending on the amount of activity. Sub folders of the Sent folder take on the characteristics of the Sent folder. You will get much better performance by doing that, and migration will probably be better too.
Then, Re-Index the important folders, to be sure that they don't have surprises in them. The new PMMail can Re-Index whole accounts, but the old one can't (I assume that your version can do folders, but it may not).
Okay, now that you have done some preparation, try it. It will ask for a new location, and basically copy all of your mail etc. to the new location (it is a new directory structure, and some files are modified to match), so be sure that you have enough space. The old PMMail will remain operational, until you decide that the new one is working. Again, READ the instructions, and remember that any mail that you SEND with one, will not be in the other. The new accounts are set to NOT delete mail from the POP server, until you set it to do so, so Incoming mail can end up in both places, as long as you process it with the new program first. If something goes wrong, you can ask what to do about it, and, worst case, erase what was done, and start over.
Another thing, is that the "Migration Tool" is badly named. It does the migration, but it also does a couple of other things, like make PMMail the default mail program, and remove the old PMMail (it actually ZIPs it up), when you select those options. It should never try to do a new migration, when the source is the new PMMail, However, if you don't have a standard setup, odd things can happen. Please ASK what to do if something goes wrong.
Oh yeah, the new spell checker needs to have the appropriate files beside the main installer, when you do the install. Page down on the PMMail home page to get the ASpell packages that you need. They are used by the main installer.
Be especially careful with existing filters. Some fairly serious problems were fixed, and that means that some filters now actually do what they are supposed to do. A few people got caught using incorrect filter operation, which now doesn't do what it did before.
You mention SPAM. PMMail now uses the BogoFilter program, so you will probably want to use that, and get rid of your own SPAM filters. I guarantee that BogoFilter will do a better job, after you properly train it (usually takes a few days, but it is not difficult to do).
That should cover most of it, but I may have forgotten something. Try it, and see what happens.