Waterproofing a GPS antena
There are dozens of waterproof GPS antennas that have elements such as you indicate inside.  Most have a LNA amplifier stage as well to compensate for the cable losses. A decade ago they were under US$ 5.00 each in 50 quantities.

When casing your antenna I would keep a few mm of space between the antenna and adjacent dielectric parts to prevent detuning.  I would also keep all metal away from above and adjacent to the antenna for at least 10mm.  The thickness of the radome on these small commercial ceramic patch antennas is typically 0.8 to 1.2mm and may even be required to get the correct frequency when installed. 

I would go with a already encased unit unless there is a compelling reason to embed it into a covert location.  If hiding it I would put a small dome to give it an air space and then cover it with fibreglass and polyester resin.