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.
UPD.
The etimology of "чересчур" is much more vague. First of all, of course, чересчур = через чур, but what is чур, anyway?
Certainly, we have the word чур as a part of "a guard spell" against the evil: чур меня! Also consider the verb чураться (to keep away, to shun). Still it helps a little, because the meaning of it is unknown. One option could be, for example, Чур / Щур (cf. Пращур) = Ancestor (so Чур меня! means smth. like Ancestors [defend] me!), but Vasmer dictionary gives this as "unlikely".
Another point is that чур меня! and чересчур may be not related in any way. Vasmer says that the word Чур, meaning a kind of Limit or Bar, is to be reconstructed from the word Чересчур. Personally I know only one appearance of the word чур in this sense: Чуры не знать means To have no limits (especially when someone eats too much). But it's a dialectal expression, and I'm not sure if чересчур is really related to чуры не знать.