Organize you folder tree in whatever way makes sense to you PM doesn't care what it is.
I tend to organize my stuff (after ingesting and processing) into folders by subject, as that makes the most sense to me. My archive folder is about 35,000 images (I'm a lightweight compared to others!).
The Tags and keywords serve several purposes:
1- When you are looking at a folder, you can include or exclude selected tags, and/or star ratings with teh click or shift-click of a mouse. For instance, if all you keepers are 5 stars, you can just select them to display.
2- If you want to search your folder on a subject (say Animals) for one particular type (say Eagles) and you have keyworded your images properly, you would just enter Eagles in the search box while you are in your Animal folder, and all of the matching tagged image will be selected. Then you just click on the filter drop down to pick "Selected" and only those images will be displayed. The search process (in Windows, not sure about Mac) only works on open folders. Once the Catalog add-on is available, presumably it will search the whole database. However, the keywords and other XMP/IPTC data that you enter through PM is available to any otehr cataloging program.
I found PM to be pretty intuitive, so my suggestion is just start using it to discover it's potential to help you. Nothing that you do in it will be wasted should you decide to switch to something else.
Also check out the Camera Bits forum, it is a wonderful resource for asking PM specific questions and learning how to do specific things you can't quite get the hang of.