I did too, no harm, no foul though. The squares were painted over or smeared with mud once the fighting started, they made too good an aiming point.
The 1939 regs had the geometric shapes as solid colours. The number you see in them is often quoted as the troop or platoon number. At least one RTR unit kept the solid shapes when the switch to outline was made in 1940 iirc. One of the RTR battalions apparently used purple instead of the usual red, yellow and blue seniority system.
Serial squares were coloured for the brigade, 1st Armoured Div had red and green for its two. Divisional troops used black. The number apparently went from generic types (e.g. all Div Cavalry used '2') to specific numbers for individual units.
All that being said, there's so much apparent confusion about these markings that I doubt it would be difficult to contradict the above.