I've read that if you restore the heating system to stock condition, it will work fine. Others seem to disagree. I haven't finished repairing my heat yet and even then, I haven't been through a Winter with that heat yet, so I can't say anything from personal experience. I can say that I am currently working on the heat system to restore it completely, and I'm considering a few modifications as I rebuild the system to make it as efficient as possible.
One site that covers the heat system is vw-resource.
They cover all the basics of the stock system.
Something else I stumbled accross was this link that shows one persons attempt to boost the system. It looks doable and I may try it. I will at least replace the "Y" connection under the back seat to direct all the heat to the front of the car, where it will be needed most. Nobody hardly ever rides in the back anyway, an it's not as thought the car is so huge they will never get warm with the heat only coming out of the front. The link I found is below. It has a pic of how his modification came out.
I can't tell you how well all this does or doesn't work. I'll let you know in a month or so. By then I'll be done fixing the system and making whatever modifications I decide on. Plus, it will start getting colder, so I'll have a pretty good idea if I it will work.