She is very cute I like the pink dress on her.

Puppetlady has it right with pinning and lining up pupils, usually at the very end you add the pupils in the puppet building process. I also pin everything on before I make any commitments (glued) to the puppet. I spend more time on my eye's on the puppet than any other part of the puppet because they are the "soul" of the puppet. If you want to continue to use these eye's that you bought from Ebay.....I would suggest that you get a basic Dremel tool and grind down the edges so that the pupils start looking at each other a little more.....this will reduce the work of having to "build them up." As a way to see if the eye's are "focused" you should stand a couple of feet away from the puppet and see if the puppet is looking back and focused on you. Henson described the "focused" method like an invisible triangle made up by the nose and pupils then you know things are lined up well. The pupils should be slightly crossed eyed without going to far by making it look like a village idiot it should look focused and looking back at people.
BTW a Dremel tool you can get for a pretty reasonable price, you only need a basic one and you can do so much for making puppets with it. You can use spoons for eyes the tool can be used to smooth out edges. You can use it to smooth out foam if you are shaping foam. I could go on with puppet making with this tool but it is worth the investment if you are interested to continue to make puppets. It is also very handy to do some house repairs or projects. The best part it is no bigger than a small drill.
I use scrape booking punches that are circles in various sizes and then I get sticky back vinyl that they use for signs ect....and stamp them out with the circles sizes I like and stick them on. I find this easy to use and gives nice clean eyes. You can also get the black sticky back material with fuzzy/velvety side to it works really well to make pupils.
Hope this helps.......