I'll echo what was said above, but add a bit more.
Center of the truck roof is best. It gets the antenna where it will work best. The roof provides the full ground plane the antenna needs to work properly. If you do it correctly now, it will outlast your truck. There is a very good reason that all the public safety and professional installations you see will use a properly installed antenna.
As for what antenna to choose, someone has probably already done the work for you. Just take a look at whats on top of the fire apparatus. Use what they used and you'll likely be in good shape.
A couple of other things.....
-The licensee on the FCC license for your agency is the only one who can authorize adding radios to the system. While you may work for the department, that doesn't mean you can add radios without the licensees permission. Make sure you get something in writing, on agency letter head, signed by the top guy, saying you have been authorized.
-Don't add any neighboring departments without written authorization. See above...
-Make sure everything is done correctly, programmed right, and set up properly. Making a mistake can cause interference. Don't be "That Guy". You never want to be "That Guy".
You can program these radios with receive only channels. It might be handy to program in the NOAA weather channels, and maybe any other agency you want to monitor. Just make sure it's set to RX only.
As for the antenna mount install, absolutely. Drill the hole, do it right and you'll never be disappointed. Seen too many guys do half way installs, magnetic mounts, glass mount, some cheesy bracket off the bed or hood. They'll work, but they look unprofessional and the performance suffers. If you are not comfortable doing the antenna mount install on your own, get someone to do it for you, it really is worth it.
Always, always, always connect the power for the radio to the battery. Never ever tap into existing wiring, or worse, use the cigarette lighter plug. This is the quick way to screw up your install. Direct to the battery provides ample clean power to the radio. If you require the radio to turn on/off with the truck, use pin 10 on the rear connector and program the radio to use the ignition sense function. You'd wire pin 10 to an ignition controlled circuit (or a timer) and it'll turn on and off with the truck.
Also, while the CDM front firing speakers are really good, consider adding an external speaker. It really improves sound quality, intelligibility and you'll have no issues what so ever driving down the highway with all your windows down.
I'll add that I'm running a CDM-1550 in my 2011 F-150 with a quarter wave VHF whip mounted in the center of the cab roof. Never had an issue with it and it works very well. The control head for the radio has been remote'd under the dash board. The RF deck (radio guts) are behind the rear seat.
The antenna is flexible enough that if it hits a parking garage roof or tree branch, it just bends over and springs right back.
Here's the CDM-1550 with a Kenwood NX-900 800MHz control head under it:
Here's the NMO mount going in. Center of the cab roof:
Here's the head on shot. This was before I added the Kenwood: