Chrome on ChromeOS is built on a mix of code sourced from Chrome on Linux and Chrome on Windows. Much of the user interface code is shared with Chrome on Windows. As such, if you make a change to Chrome on Windows you may find your changes affect Chrome on ChromeOS. Fortunately to test the effect of your changes you don't have to build all of ChromeOS, you can just build Chrome for ChromeOS directly on Linux.
First, follow the normal Linux build instructions as usual to get a Chromium checkout.
Now, once you build, you will build with ChromeOS features turned on.
Note that when you build ChromeOS Chrome, you'll be using the TOOLKIT_VIEWS frontend just like windows, so the files you'll probably want are in src/ui/views and src/chrome/browser/ui/views, not src/chrome/browser/ui/gtk! Also, if chromeos=1 is specified, then toolkit_views=0 must not be specified.
Note also the underscore in the GYP_DEFINES variable name, as people sometimes mistakenly write it GYPDEFINES.
To specify a logged in user:
Look at the ChromiumOS documentation for the official flow for doing this - you will need to check out the ChromiumOS sources and create a chroot.