I would avoid using "enclosed it in" because, for me "enclosed" already contains the meaning "in". It seems tautological - it isn't, really, but it still jars to my ear somehow. I guess I'm fussy but it doesn't sound elegant to me.
Like riquecohen, I like "enclosed with" - I think because one doesn't really enclose something "in" an application; one puts the application and the other item in the envelope together. An application can't enclose another piece of paper. If you have stapled it to the application, it's attached not enclosed.
If I prepare an application (a single piece of paper), fold the paper and insert my business card into the fold - didn't I put the business card in the application?