Christian,
JFBConnect will attempt to resize the page automatically. This is a very dumb attempt where we basically force the body tag to 780px (for Canvas) or 520px (for Page Tabs). In most templates, this works reasonably well, but it's not always perfect.
Alternatively, you can disable JFBConnect's resizing which should then simply add scrollbars to the 'frame' of your page when viewed within Facebook. Not always ideal, but can definitely work just fine.
In the event that you don't like either of the above, you can copy your current template and make some modifications to it, or use a simpler template altogether. JFBConnect let's you select the template that you want to use when displayed within Facebook and then you can tweak it for that environment however you want.
Hope that all helps,
Alex