I'm not sure if I understand what you mean by 'certain folders'. Either way what you probably want is a smartlist--an playlist updating manually.
Fx. let's create a smart list containing all files from the folder C:\my music\, containing the genre-tag 'rock' and is older than 1990. Cf. the 'Smartlist and Search - Rules and Modifiers'-article in the help file we can define the smart list as
g=rock , location="C:\my music" , [Date (year)]=<=1990
Now, we want to make sure this playlist is synchronize automatically wwhenever your iPod is connected.
First, go to Option (ctrl + o) and go to 'Handheld'. A plugin for the iPod should be installed; make sure it's selected from the top-drop-down-box. Click on the 'configure transfer option'-botton. Click on 'Auto-Sync Only these playlists' and select the playlist we have just created.
Either way, the absolutely best way to manage what songs are on your iPod is described in Larry's iPod Notes (http://yabb.jriver.com/interact/index.php?topic=22729.0). For some reason it has been unstickied.
Ta-ta,
R.