What you need to do is create two separate .sx files (menu documents) for both menus. There are a few important settings which must be set in both documents in order to get the menus to work together.

First of all, you need to select the option: Output / Multiple Menus Support. Then, for the first menu, set the option: Output / Multiple Menus / Menu ID to "1" and for the second menu, set this option to "2". Please note that menu ID's must be different for each generated menu and must be incremented from 1 up.

Then, you should set the option: Output / Optimize size of generated JavaScript files. If both menus have identical functionality, use the same effects and features (e.g. fading effect, bitmap-based menu bar) you can set this option to "Yes" which will cut down the size of the generated JavaScript file. However, if the two menus use different settings (except for fonts and colors which don't have an influence on this option), you must set this option to "No". If you are in doubt, choosing No is the safest option. Of course you can try setting the option to "Yes" and verifying if both menus function as expected.