Seen from a distance they were usually flippin' well identical and a lot of them had no differences whatsoever.
However, a very few regiments used a 'pile wavy', which was a wavy flame-shape in gold, extending diagonally downward from the canton (i.e. the top corner nearest the hoist). The II Bn would have one pile wavy, the III Bn would have two and so on. However, this was very rare by the Napoleonic Wars and I can only recall it being carried on one of the colours of the Foot Guards and some Militia regiments.
One Highland Fencible regiment added a broad red horizontal stripe across the centre of the Regimental Colour of their II Bn.
Most commonly, regiments would add a Roman numeral 'II' or 'IId Battn' in gold on the canton or centrally above or below the central design.
I can't find anything specific for the II/88th, although they do seem to have put '88' in the middle of the small Union Jack in the canton of the Regimental Colour.