One thing to remember about RUb fatigue is that fatigue stops when you go above 32x TC. Consequently it's best to do any cruising to and from the patrol area at 32x or higher.
You'll also need to make good use of officers and crew with qualifications, as RUb makes effective use of qualifications much more critical than under the normal SH3 fatigue system. Avoid wearing out crew with qualifications unnecessarily - keep them in the barracks (where they won't tire) until they're needed to supplement sailors who are tiring.
After a patrol or two, your crew should be experienced enough that fatigue doesn't become much of an issue. I soon found myself having to do far less micromanagement than with stock fatigue.
Edit: What a frighteningly similar double post!
