First off, to give some credentials, I've been a Master installer, MECP certified, and done installs in thousands of vehicles over the years. (Just so you know I'm not talking out my ass.)
The Viper security packages are designed around a Toyota vehicle's electronics, believe it or not. Meaning, the Toyota line is the first one to undergo testing from the R&D facility at Viper. This is due to the advanced electronics in Toyotas that usually leak down to the domestic market far after Toyota has improved on the design already.
Viper designs them to work around the stock alarm systems, locking systems, and all other stock options. If installed properly, nothing should ever show a sign of conflict.
In the car audio industry, we frown upon Best Buy and Circuit City's installations, due to an abundance of shortcuts and money-saving performance-compromising parts. However, each individual location must have one installer, the "master", who actually knows what he's doing. Talk to him before allowing them to install. If you're nice to the installers, they'll usually NOT skip on the "optional" steps, like setting sensor gain and programming options that are usually "not included" and can be very hard to do without a background in automotive electronics. Still, for most people, these retail install shops will operate and install fine. Circuit city installs RADIOS better than Best Buy, typically, although I'm not sure about alarms.
So, in summary:
-If installed right, no stock electronics should be harmed or cause problems. You should also NOT lose any original features.
-Retail installers are fairly cheap, and moderately reliable, but trade secret of talking to the master installer first usually will get you a better install, or even a discount on time.
And yes, I'd go with the best Viper alarm you can afford in your budget. Viper is a great product line and has good quality control measures.
Hope it helps! Feel free to message or post reply if you have any questions I might be able to help with.
-Tom
