A heat gun should always be the first weapon in your arsenal against a tricky floor adhesive. It may be particularly useful when you're lifting the old flooring, which was most likely some sort of vinyl, linoleum or carpet if it was adhered to plywood. As you lift the squares of old flooring, blast the heat gun onto the adhesive to soften it. If you're lucky, the adhesive will stick to the old flooring instead of the plywood subfloor.
Many chemicals on the market are designed specifically to break down old adhesives so you can remove them without wrecking the subfloor. Mineral spirits work well, as do products containing acetone. Both of these, in addition to other solvents, are available at home improvement and hardware stores. Although the directions may vary, most manufacturers instruct you to pour a small amount directly onto the adhesive and let it sit for a few minutes before you try scraping it up. Remember to work in a well-ventilated area when using any type of solvent.
Once you've softened the old adhesive, you can start scraping it up. Since you're working with plywood, you should avoid using metal tools for scraping the adhesive so that you don't damage the subfloor. Hard plastic putty knives work just as well and have a much lower risk of damaging your plywood floors. This tool is pretty straightforward -- just place it against the floor and scrape the adhesive until it lifts up. You may need to apply more solvent as you work.
Sandpaper should be your last resort if you can't remove the old adhesive with the other tools and solvent, or if you simply have a few stubborn spots where the glue just won't budge. If this is the case, allow the solvent to dry and rub the stubborn spots with rough-grade sandpaper. Anything around 100 grit or lower will do the trick since you're not trying to smooth the surface. Sand away and keep checking to make sure you don't start sanding the subfloor surface.