If you have the ability to put the holes in the case on the bottom, that’s the best method to prevent water intrusion. Then you have a choice: (1) You hang the antenna upside down from the bottom, or (2) You have a feedline and put the antenna elsewhere. If you do this, get good quality feedline and beware of attenuation losses, which are really high at these frequencies. I use LMR-400 with N connectors. If you can only put the connector on top, use some kind of real gasket or RTV sealant, and design the case such that you know it’s going to leak. On the inside pigtail, put a drip loop on it so that water won’t run down the cable onto your radio. And put a case vent / drain on the bottom of the case. In any event, any connector that is exposed to weather should be tightly wrapped with self-fusing silicone tape. Just remember what @ziffzuh said: The most important thing (besides the case not leaking) is to get the antenna into an unobstructed vertical space. If it’s right next to a metal pole, it won’t work as well.
This is an example at SKYLINE. All the case penetrations are on the bottom of the case, the N connector is sealed with self-fusing silicone tape, and all cable entrances use sealed cable glands. I installed a short feedline to the antenna mounted just to the right and above the case. LMR-400 cable with N connectors. You have to calculate the feedline loss for your system if you want to know the total EIRP power output. LMR-400 is one of the lowest-loss cables available to the hobbyist. Attenuation at these frequencies is -1dB per 25 feet.