You can reorganize the folders and where emails are stored while you are viewing the emails that you’ve downloaded. However, when you go to download new emails, WAM will read the folders as they are in your webmail (at your email providers server). All you have to do is download them, and you can move them once they are in WAM.
If you don’t want to have to move your emails or folders after downloading, just change the way you have it organized in your webmail to match the way you have it in WAM. Then they will download to the same folders.