The custom_1 and custom_2 positions were specifically built for the S5 Image and Content Fader module and the S5 Tab Show module. When both of these modules are used in these positions on the same page the S5 Tab Show module will overlap the S5 Image and Content Fader module, and the S5 Tab Show module will fade-in (as seen on this demo's homepage). These features will only appear if both modules are published to these positions on the same page. That does NOT mean that these are the only positions you can published these modules to nor does it mean that both modules must be present on the same page, it means this is the only configuration where the overlap and fade-in features will be present.http://www.shape5.com/demo/oasis/index.php/features-mainmenu-47/template-features/92-module-positions
Because of the integration of these modules the custom_2 position should ONLY be used for the S5 Tab Show module and no other module, it is laid out just like the top_row positions and those can be used in its place for other modules. Custom_1 was specifically built for the S5 Image and Content Fader module but you can publish any other full width module there as well, but keep in mind that the menu will over lap this area, so an image module fits this area best.
I would have to see the effects live to take a look at the source code. If you can upload it to a temporary server I can see whats going on for you. Without seeing it the only thing I can suggest might be to adjust the widths in case you are having an overflow issue.