Remote and testing server don't see root relative links the same

My site works fine on my testing server (Apache, MYSQL,
PHP). I use root relative links in a library
file (include file) so that it will work with all pages. For the testing server these links look like this:
/my_sites_root_folder/aaa/bbb/ccc etc.
If I use these same links on the remote server they won't work. To get hem to work I have to change all these links to the form
/aaa/bbb/ccc etc.
When dreamweaver uploads files to the remote server, the site name folder  (my_sites_root_folder) doesn't go along for the ride--just the files in it. So on the remote all the site files are stored in htdocs. On my testing server, the files are stored in htdocs/my_site_root_folder.
I think it must have something to do with the way I'm setting up the remote and testing servers, but I'm read a hundred pages of instructions without being able to figure it out. I think I'm just seeing something wrong, but I've already spent days on this. Can someone please point me in the right direction?
I'm using DWCS5. Internet explorer 8, Windows 7.

Thank you for your prompt response. I'm afraid I'm still totally puzzled here. It sounds like you're very knowledeable about your comments, but I would like to know more. I accept that using the local site root in links would be bad, but I'm not clear WHY. Structuring the links as I have doesn't cause any links to break. I've structured them this way because it's the only way I can find that everything works. But I still do not understand WHY I have to do it. Using different libary include files doesn't seem like a good way to go, though
You suggest that if I use any root relative links at all, I need to use vitual hosts. I'm not finding any good coverage of what these are, and especially why they are necessary. If this is the case, does that imply that templates (which use root relative links) also will not work on the test server (at least without vitual hosts)? The conclusion I'm coming up with, given your remarks, is "Dreamweaver doesn't work with root relevant links when you're trying to test a site with a test server." Is this right?

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