The identity of rōnin changes throughout the period. The term is usually used in the Edo period sense of a 'masterless samurai.' Such rōnin struggled to find employment due to the absence of war, and lords not needing to keep too many retainers. After 1590, with the country unified and Hideyoshi's laws separating the social classes, and most crucially mandating that warriors live in the castle towns, it's this kind of rōnin that emerges. Sekigahara in 1600 and the two Osaka campaigns in 1615 are flare-ups in an otherwise peaceful period.
Prior to Hideyoshi's reforms, a rōnin was any wandering warrior who may have been ejected from his land, left his village due to famine or poverty, or left the service of a lord. In one of his letters, Hideyoshi describes himself as a rōnin from after he left the Imagawa and before he joined the Oda. In the Sengoku period, these rōnin could find employment much more easily than later. Along with semi-independent small landholders and village troops, they would fight on a part-time basis for pay or the chance of future employment. All these men would most likely have been grouped together for battle.
So, for example, if a lord brought 1,000 men to battle in 1560, he would have some permanent warriors, a core of troops provided by his closest retainers who always turned up, and then some of these part-time troops from areas that he only had nominal control over. As the period goes on, or as individual daimyō exerted more control over the areas they governed, those independent land-holders and villages are brought more and more into the daimyō's system of government and so the ratio of permanent and close retainer warriors increases. Obviously this 'regularisation' varies greatly throughout the period, both in terms of the year, and the part of the country.
Those rōnin and others would most likely form their own ad-hoc units. But they would still be part of the 1,000 men provided. So it really depends on the scale of your game whether they are considered separate units. Basically, if you're grouping troops by same weapon type, then they're separate units. If you're grouping them into 'sonae' then they're part of the unit. They may have had banners appropriate to the lord, but probably not sashimono. Individual warriors may have worn their own sashimono, whether they were rōnin or small landholders. Personally, I'd do these as a mix of troops, with a variety of quality of equipment possibly with a few different sashimono dotted throughout the unit, and with the same, or similar, nobori banners as the 'regular' troops. They'd be of variable quality, and harder to command.
The Osaka campaigns are slightly different due to the different social standing of the rōnin. They will have been assigned to individual commanders, who probably equipped them with flags and sashimonos. Sanada Nobushige famously equipped his men in red armour, most of these would have been rōnin (the Sanada clan troops were fighting on the other side for Nobushige's brother). In this case, I'd be inclined to just do them in appropriate sashimono (if they're wearing any). The rōnin at Osaka were probably better motivated than the earlier rōnin as they had nowhere else to go, and many had a grudge against the Tokugawa. I suspect that they were pretty well integrated into 'regular' units, but I don't know much about the Osaka campaigns.
