Ok I think I understand clones a bit better now and you're right I can do exactly what I want with them even if it is a bit clumsy. Here's my current method, feel free to point out better ways i could do this:
1) create a blank document, in my case I want a 100x100 px file
2) create a 100x100px rectangle and position it at the origin
3) create some random object ontop of and smaller than the rectangle
4) group the rectangle and the random object
5) create a 3x3 grid of tiled clones of the group
6) move the original group out of the way for the moment
7) select all the tiled clones and shift them so the middle clone is positioned (top left) at the origin
8) delete the random object from the group as it is no longer needed
9) start drawing on top of the original rectangle making sure new objects are added to the group
10) draw some cool tileable stuff
11) unlink all the clones
12) ungroup all the outer cloned groups
13) delete anything that doesn't overlap the document
14) finished!! your document should now be a seamless tileable chunk of svg coolness