I can not answer for those families specifically, but in battle only the main clan's banner is flown. You can see Shimazu's cross in circle clearly in this drawing of Sekigahara. But as mentioned here you can pretty much do whatever the heck you want with your armour, and one of the things you would be likely to personalized would be the helmet with those fancy designs.
In the Edo period, while low ranking retainers seemed to have worn unmarked clothes or that of the clan's crest, high ranking retainers of a clan seemed to have worn clothes and marked baggage with their own family crest. You can see them in the various drawings of daimyō entourage:
New years greeting to Edo, what looks like Kaga domain (Maeda) on the right and one of the Gosanke (Tokugawa) on the left. Note the people on foot with colourful haori that have different crests compared to the people wearing plainer haori.
