I am glad you decided to give mojoPortal a try. I think you are going to love it!
I am assuming you normally use the inline frames approach so you don't have to worry about keeping your menu up-to-date on all your pages. The good news is that mojoPortal handles your menu and ensures that the root menu is on all pages. Another great aspect of mojoPortal is it is possible to have your menu horizontally across your pages or vertically on your pages.
If you haven't already installed mojoPortal, I suggest you take a look at the demo site (http://demo.mojoportal.com). You can login to this site with the username firstname.lastname@example.org and password admin. Once logged in, click on the Administration link and then on Site Settings. In the site settings there is a link next to the skin selection box titled "Preview/Browse". If you click this link, you can browse through the skins that come with mojoPortal. Some of them have vertical menus and some of them do not.
I hope this answers your question.