Just done one last week and exactly the same with the small squares, they were a good 2 or 3mm bigger than the corresponding rectangular tile, ended up using 4mm spacers on the larger tiles and just red wedges and rack of the eye around the small square, not a lot else you can do really... I wouldn't get too hung up on it tbh as you'll notice once you finished that its about the overall look of the floor rather than individual lines and joints..