Yup thats the trick, we would use wax and grease remover for paint and just scuff the rubber seal with 40-60 grit sandpaper and clean the rubber with the wax and grease remover and use sandwich bags or cellophane and put the silicone on the rubber or where you needed it to stick. You rework the silicone as it sets up with your finger and saliva.
For some reason saliva works very good for reworking the Silicone as it sets up and keeps the silicone from sticking to your finger. Have plenty of paper towels handy to wipe up the excess Silicone, (and slobber) only wipe 3-6 spots of silicone per towel, that stuff travels. If you get too greedy cleaning silicone with one towel you will look around and see that its on everything. Throw the paper towels away earlier than you would if it was grease. That stuff has legs and before you know it you will have gotten it on the interior of the car or on your clothes.
Let the silicone set up about 10-15 minutes then shut the door gently (sometimes not even all the) way with the bag material over the uncured silicone let it setup. Look for spots that will need to be reworked from the inside and out and keep reworking it with the door closed.
Don't do both sides the same day unless your extra clean and careful. Also do the passenger side first you will surely be more experienced on your side. Within a couple of hours you have a leak free car again. Once you get good with working the silicone you can make some pretty complicated shapes and make it do what ever you want.
BTW humidity helps cure RTV so the saliva really has 2 purposes.