i'd say, depends on how the code is structured and what you need to do. mootools does render itself to easy refactoring and extending (this is, after all, partly the reason it exists) but it takes a while to figure best practices and so forth.
however, your learning curve from vanilla javascript or jquery won't be too steep, especially so if all you care about is DOM mantipulation, event handling and effects. things get more interesting when you decide to write / extend mootools classes and venture into prototyping - but you may not have to do that...
there are some pretty good tutorials around for most things as well as some demos on doing things through jquery and mootools (equivalent ones). http://jqueryvsmootools.com/ is a good example on how the same task can be done through either one, i'd recommend reading it before deciding.
whatever you decide, it is a bad practice to use two frameworks (when you can do without).