ALL mortgage companies use all 3 bureaus
Dealers or small store credit card issuer may use just one or two of the 3 major credit bureaus to save on subscription fees, but with home loans – no lender can afford not to check your 3 reports. You won’t find a mortgage company that uses only one or even just two bureaus.
Normally, a mortgage officer will use your middle score (which in your case not so good).
However, what you need to understand is that the Fico scores that you have are NOT the Fico scores that the mortgage officer sees, so you have no idea what are your “Real” scores.
Fico scores have 3 versions: “Standard” (the ones you have), “Auto Enhanced” (that car dealers use) and “Factual” that is used by mortgage companies.
As a consumer you have no access to the Factual score, which by the way tends to be a little lower than the standard version that you have (See understanding-fico-scores.html for more information).
Simply apply and hope for the best.