true that,
Always test for continuity anytime you make a change.
If you are moving components to under the seat. Lay the harness out on a sheet of plywood/cardboard/drywall as it would have been on the, with the components in place. Take a photograph of that. take detail photographys of the connectors to the components and wiring colours. Sometimes you'll have extra wires not connected to anything necessary for your bike. Mark these for removal and remove them.
Position you components where you want them to go in relation to the laid out harnes, and starting at one component at a time, unravel the mess that is your harness. cut, solder and splice the wires to where you want to the components to be.
The whole time, test to make sure there is continuity from connector to device.
Sorry if this isn't a cut and dry diagram for your exact harness, but when you start cutting into a harness there rarely is. Just make sure your connections are good, your wires are soldered well and you shouldn't have much trouble.
On my cb650 there was a few extra wires and then I installed a yamaha key switch (3 wires) to the honda harness (5 wires). Lesson in diodes on that.
Good luck.
There's also the 650 forums which will be more specific for your needs.
http://www.xs650.com/forum/
Good Luck
Jay