I am looking to deal for a player that has 3 years left on his deal.  I have plenty of payroll this year, but next year am 65k over the payroll with his salary.  I really don't have much way to deal back any players to get under, so my question is if I transfer over from prospect budget, will that extra million I get for this year also be accounted for next year?  

It will increase next year's payroll but not by a full million.
Next season's payroll is limited to some % of this season's payroll.

So yes 1Mil added to this season's payroll should be plenty to cover a 65K shortage on next season's payroll.