I'd recommend replacing the brushes around 100k-120k miles. That is about the point where they start to wear thin and cause alternator problems. Most alternator problems are just the brushes wearing out. On the Beetles you must replace the brushes and voltage regulator as an assembly. Costs around $60 and is fairly easy to do. The hardest part is getting the alternator off, which you will have to do anyway to replace it.
I have a 2000 new beetle that started to have problems with the battery staying charged. It will take a full charge and runs good but ounce I have turn it off overnight the battery is real low or dead. My question is should I replace the battery first or the altenator.