finished the lantern tutorial yesterday, although there were a few areas where i got different results it was a good overview of substance

question:
i am trying to apply what i have learned to my own model now:
-but in the baking process, my model does not have a model with id's like your lantern.id version did-
my model is an obj, and the automatic uv unwrap function appears to have done a decent job with it [although it grouped up a lot of the separate surfaces into a single one] so substance is seeing different surfaces for it...
i tried using the low poly mesh as high poly mesh [i only have the one] and because substance was needed to create my UVs, i am getting a pile of errors being thrown.
what are my options here? I need to bake out the mesh maps, but i can see while it is processing that they are far from correct. when it finishes, they are definitely messed up.
i am quite new to this process and have no idea what to expect here, how to proceed.
thank you,