There is an open source Eclipse plug-in called Subclipse which adds support for Subversion to Eclipse which may help you a little by integrating SVN with eclipse.
Obtaining & Installing Subclipse
Eclipse plug-ins are downloaded and installed from within Eclipse. Open Eclipse on your machine (it does not matter which workspace you open).
From the Help menu select Install New Software…
In the resulting Install dialog enter http://subclipse.tigris.org/update_1.6.x as the site address and click the Add… button.
Enter a Name for the site like Subclipse
The new name you chose will show up in your list of sites. Ensure it is the only entry checked and then click Finish.
Expand the Subclipse entry which shows up in the window that pops up. Place a checkmark next to the Subclipse (required), Subversion Client Adapter (required), JavaHL Native Library Adapter (required), and the SVNKit Client Adapter (optional) sub-entries under the URL and click the Next button.
Click Next
Accept the license and then click Finish. Eclipse will now download and install the Subclipse plug-in from the project’s server.
You may receive a warning about unsigned features, if you do choose OK to continue the installation.
Once the install is complete you will be asked if you want to restart Eclipse, choose Yes.
Using Subclipse is like using the default Eclipse CVS client. There are a large number of walkthroughs and manuals available online. A Google search for ‘how to use subclipse’ is a good place to start.
Edit: As pointed out by a very helpful commenter Lombo you can also auto add files to SVN when you use Team -> Commit on your project, I was not aware of that function, thankyou!
Edit: If you want to know more about SVN check out this link from IBM. They have a section that deals with ignoring files which you may be able to bend to your needs of not auto-adding certain files. I think the Team > Add to svn:ignore functionality may be as close as you can get without playing with the command line SVN.