Well, the difference is in negative form:

For example, _Он не слишком умён_ means _He's silly_. Yet negative _не чересчур_ is almost never used except questions: _А не чересчур ли он умён?_ etc.

Also _с лишком_ literally means _with excess_, so if written as a whole _слишком_ is an adverb, but separate _с лишком_ is a noun.