You didn't mention what type of antenna you're using, I assume it's a 1/4 or 1/2 wave whip. The best place is centered over the largest flat steel surface you have, that allows the whip to have a ground plane to radiate the best signal. Mag mounts are popular on a roof, another good spot is on the hood. The "higher the better" theory certainly applies to your base station, however a mobile really isn't that critical, you're only talking about 3 feet.
Wave propagation of an omni antenna radiates in 360 degrees, if you could watch it the pattern would be like a ball exploding in all directions. A metal surface causes an immediate bounce or radiation. That exploded signal acts on the atmosphere and reflects toward the ground, we refer to this as "skip" allowing your signal to bounce further away than your line of sight transmission.
In a convoy, where coms are short, less than a 1/4 mile or so, with 2.5 watts you shouldn't have a problem with line of sight. At 5 watts you should peg the receivers "S" meter.
With line of sight your "stick" is looking at another "stick" anything in between the two can cause a poor signal. Putting your antenna in the back, say on a bumper just creates signal interference forward of the vehicle. Placing it low on one side can block transmission away from the other side. The metal of your vehicle reflects your signal away from that surface, like a mirror. The earth, heavy clouds and hard surfaces reflect radiation.
The lower the frequency the more radiation can occur which is why the 160 meter band is better for DXing or long rang transmissions, higher frequencies don't "skip" as far. Low frequencies have a longer wave length, the higher you go the shorter the wave length.
The wave length is what your antenna is "cut to" or "trimmed to" a vertical or horizontal dipole is made to fit the frequencies in the band you operate in.
You can use a 1/4 wave, 1/2 wave or full wave generally, I say generally because there is equipment that artificially tunes different lengths to the desired frequency, yes, without being a smart a^^, they are called "Tuners" You can tune a wire fence as an antenna, there are HAMs running a half mile of wire fencing, or more that get really great results.
So, back to your best location, for mobile operations the center of your metal roof is best, next would most likely be the center of your hood, I'd guess that part of that stick would be above the top of your vehicle so dead space to the rear shouldn't be critical. Glass doesn't interfere with a signal very much at all.
Disadvantage: Height clearances, a metal whip will bend down as it drags under an obstacle, like a tree limb. A drive through probably won't hurt it, but going in your garage then backing up will twist the whip, you can damage the mount connection or it could pop off.
Which is why mag mounts are popular, slap it up there when you intend to use it, you can even leave it on and just take it down as the situation changes. 73's
