I have a 56 page pdf file set up as single pages with crop marks and bleed so the finishing size should be A4.
How do i put the covers into indesign from the pdf file and to set up correctly i.e with spine and crop marks and bleed.
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It really depends on the thickness of the paper you print on and the thickness of your cover.
I would recommend you talk to your printer to ask what he/she recommends as it might include the returns to wrap around the cover pages.
I used in the past a great plugin from http://blurb.com that adds the correct amount of space for the spine depending on the amount of pages and the thickness of the paper selected.