Good question Goliad! I've often wondered that myself. How did the High Command deal with the large number of Ronin? Were they just parceled out to various commanders?
I have a bunch of books on Samurai, but none of them address this (not even Turnbull!). I would assume they would wear the Sashimono of whatever commander they were under (?). A number of the Daimyo used blank coloured Sahimono and Nobori so maybe the castle had stocks of plain banners (?) or had them made on site for the troops (?). Too many questions.
I know Mori Katsunaga's force was made up largely of Ronin...but were the rest made up largely of Ronin as well? There were other leaders there on the toyotomi side that didn't really have their own "Clan forces" either like Ban Naoyuki (Ban Naotsugu), Chosokabe, Kimura Shigenari, and Goto Mototsugu that I know of - there may have been others too. It's a very interesting question, and hopefully someone somewhere knows.