From the low-poly object, bake a color
map to isolate areas for masking in
your paint program. To texture, open the
baked map in Photoshop and create
selection areas using the Magic Wand
Tool before painting.
Similarly, assign it as a color map to the
low poly object in a 3d paint program
like BodyPaint. Again, to isolate sections,
use the colors to select areas then
create painting masks from the
selected area before texturing.