This tip assumes that you have already configured XFree86 to work correctly on your computer; the only problem that you have now is that you have a dual boot system Windows/Linux + Xfree86 and that the standard resolution that you are using in both OSes is not displayed exactly at the same size/position.
If you have an advanced monitor you can just set the desired parameters in both windows and XWindows; your monitor should remember the settings.
For those of you (including myself) who do not have such a monitor:
The solution is called xvidtune. It comes pre-installed in Debian and Slackware distros. Once you are in XWindows start a console and from there type: "xvidtune". Click OK to the warning message - the newer monitors cannot be damaged by settings manipulation. Now use the bars to adjust the size & position of the image; when you are done press the "Show" button. On the console's line you should see something like:
Now edit /etc/X11/XF86Config. Pay attention: on X11 v4 the config file is called XF86Config-4; on some systems you have both files - even if only one is used. Just make sure that you are editing the right file. Now go to the section "Monitor" and add there the above line with the prefix modeline as follows:
I will just copy & paste my own "Monitor" section so that you will get a better ideea:
I think that you have spotted the only modeline in the above example:)) Of course you can add more modelines for the other resolutions that you are using.
If you where not able to start XWindows at all, the above info is not going to help you; you can configure X11 with xf86Config; I know that there are other tools available; just use the one that you are used to and start X11 then use the above information to fine-tune things.