It should be possible to set jqMarquee to start outside of view. "startVisible" should be the option you are looking for. Try to set it to 0 or false.
Please ask again if it doesn't work. It is some time ago, but I also made experiments with it.
If your content is pictures only you could use a widget I posted in another thread some time ago. If you are interested just ask and I will try to find the thread.
If I remember correctly the current version of jqMarquee is buggy for vertical scrolling, but I'm not 100% sure about that. Would need some testing I guess. If you give some more information on what is included in the marquee I could try out a little bit.