The process will only overwrite files of the same name. You will find that most addons just add new files to the folders, so none are overwritten. The folders you drop in, will merge with those that already exists, not replace them.
The only time I have ever actually overwritten exisiting files is when I'm repalcing default textures with hi-res ones or something similar. Well produced addons will tell you if the installation will replace any exisitng files.
One thing to consider: Since Orbiter is just an unzipped set of files it is very easy to have multiple copies on your HD. Many orbiteers run several copies for different addon compilations. e.g. NASA historical, Hi-res, futuristic sci-fi, etc. With one that they use to test new addons to check they do not damage or change the file structure. If it works on your test bed then you can safely install it onto another one without worry. It is worth running orbiter each time you install a new addon to check for incompatabilities, rather than adding 15 then running it. Makes bug hunting (should it be necessary) much easier.
Lastly, some addons which use mfd functions and such, will also require you to activate a module in the module tab of the orbiter load screen. Some addons will also require other tweaks to work. Best rule I can give you is read the addons enclosed instructions. All good addons will explain any steps you need to take.
The manual approach required is a reflection of the fact orbiter is free. Plus the community is great, so any specific problems you have, just ask here.
hope that helps