The problem depends heavily on how you target your CSS styles - e.g., if you use an ID-based selector, it would always override the ones in the RadMenu skins due to the higher specificity of the ID selector.
A way to work-around the problem is to target your styles more specifically (e.g. wrap the necessary li-s with a container that doesn't include the RadMenu.
If you need further assistance, please open a support ticket and submit a live URL / sample project so that we could give you more specific advice.
the Telerik team
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