Use the correct windscreen sealer, spray sopy water on the paintwork and seals before pushing the tube under the seal, seal up and scarpe off excess with a plastic spatula, dont even consider silicone sealant. And if you seal it up it also helps stop creating a watertrap for the rust to reappear...
I was advised to use window fitters Sikaflex on the notoriously leaky double glazed back screen on my Westy (after a large amount of the bottom lip and the inner skin of the back door had been welded up as a result of it leaking previously). Did the job on Saturday and it appears to have sealed perfectly. I think the stuff cost about £8 (it's black so matches the seal) but it's quite a messy job.
Silicone just doesn't seal as well for some reason, one reason being it turns hard too quick, u need a flexible sealant - believe me I have tried quite a few over the years. Go to a motor factors and ask for a tube of windscreen sealeant, mine was less than £3! The fact it's black also helps...
If the rubbers have a lace in the middle of them which they should do if its a panel van converted you should seal them body to rubber and glass to rubber.before you put the lace in. if there original or replacement vw seals they are self sealing rubbers so you wont have to seal. If you need sealant go into your local autoglass depot and buy or blag a tube of Arbomast sealer off them.
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