Engine swap question!!!!! Need to know some basics

I'm having a engine swap done in my base model rsx coming out is a k20a3 going back in is also a k20a3 I would rather a k24 or at least a a2 but a little strapped for cash and it has to get done now. So I have to find the engine buy the clutch and take it to my Honda guy....I found a base rsx with a k20a3 in it but it's a 2006 automatic....I have a 2002 manual.....question is will this still work????? Will I need to switch ecu? ???? What are things I should check to know the swap will go smoothly as possible???? Thanks in advance this forun has been a huge help...new to the tunner world can't u tell lol

Engine swap question!!!!! Need to know some basics