To clarify, it wasn't on Tobe's bed that the indentation and hair was found; it was on a bed up in the attic. On the other pillow was a rotted skeleton of a human man. That's a pretty big clarification to be made. The bed itself was behind a door that was closed shut and very difficult to get into; they almost had to break it down to get in. This implies that Tobe, the servant, probably didn't really go in there, or the door would have been easier to open and close.
In the room, they found the silver toiletries that Emily had gotten for Homer Barron years before, along with a man's suit. And, of course, the rotted corpse, who was positioned "in the attitude of an embrace." The fact that Emily bought the toiletry set, then bought arsenic, and then Homer Barron disappeared, and then her house stank for quite some time, all can lead us to believe that she lured Homer to her house, poisoned him, positioned him on the bed upstairs, and then spent a good deal of time lying next to the corpse. The gray hair and indentation was hers, but next to Homer Barron's dead body, not on Tobe's bed.
It is a highly disturbing ending, one that reflects just how deep Emily's issues of commitment and abandonment went. Tobe was not her lover that we know of, and as soon as he could, he bailed town after she died. I hope that helped; good luck!