I didn't get the ending of the season two finale of dollhouse? Did echo wipe herself ou did she put paul into her head...?

She put Paul in her head. She's still Echo, he's just one of the people she has in her now, so she can still in a way be with him. We see her put the wedge in before using the chair :)
I've never been a fan of the Echo/Paul relationship, but I have to admit, I thought that was kind of sweet, and suitably twisted for them.

She put him in her mind. Now that was left for her. Did Topher leave it for her?

Well, Paul died, obviously. But since he had been 'recreated' I guess toi could say, par Topher after Alpha 'brain-killed' him, his brain was on a drive. In the finale, Alpha was good and he left Echo, Paul's drive and since Echo is special and can have many people in her head at once, she could easily put Paul there and so he'll be there with her forever. :) Happily Ever After, sort of. :P

Echo imprinted Paul into her mind, so the two spirits can live in harmony for the rest of Echo's existence.
Echo is still Echo, as Echo has immunity to the wipe, so that she can take on any personality, while keeping her own. so she was not wiped, as most people need to be in a blank-state before being imprinted, but she can withstand the print and add the new persona to the mix and control it.
- some think its creepy, but i think its really sweet.
how closer u get, than being in someones elses mind, especially the one toi love