I owe $40k on 2006 & 2007 back taxes to the IRS. I am currently making monthly payments to them now and am current. If my wife and i (who married 3 yrs ago) want to fil married filing jointly for 2008 taxes, will she in any way be liable for my back taxes where we filed separately?
No. Signing a joint return only makes both spouses liable for the taxes attributable to the taxable year of such return.
The previous answer is certainly correct. I would also add that in the event you miss a payment on your installment agreement or otherwise default, the IRS can take collection actions against you. For these reasons, it may make sense to maintain separate bank accounts and don't commingle your assets until you have resolved your prior tax issues.