My Mk2 Golf's sunroof drains via two tubes that exit in the front wheel arches. I keep them clear by running an old clutch cable down them every few months and then checking they are clear with a jug of water.
Another reason footwells collect water can be a perished windscreen seal. The seal can be made watertight again with mastic/bathroom sealant, or by fitting a new seal.
I was horrified last year to find that my local VW dealer's labour charges are £85 per hour + VAT and they charge a minimum two hours labour. Presumably they thought I'm one of those people who knows nothing about cars but I do all the work on my car myself. VW quoted me that labour charge to change my distributor last year. It's only two pinch bolts, fitting a new cap and then resetting the timing. It all took me about 25 minutes (including drinking tea), but VW would have taken over £200 off me for that!