First, there is a Research Paper from the House of Commons Library concerning the bill, available as a PDF, see Research Paper 09/42.
Written evidence has been submitted by various organisations, all listed there.
Among them are these:
Proposed amendments to the bill can be found here (click on Show+ Amendment Papers and Proceedings).
Ekklesia published on 2 June a study by Savi Hensman The Equality Bill 2008-9 and church responses to it.