Module issues!

I have a worry!
Basically, I need an A in Maths and just a pass in Further Maths..
The modules are interchangable, but who gets to choose!
Obviously I need all the best scores to go into normal Maths, but could college average them both out so I get like two B's?
If they did, I will definately fail my offer.

your college won't do it, the exam board does it automatically. They'll make sure you get the highest possible score in the Maths A Level and then the other modules will be put into your Further Maths A Level

I have a worry!
Basically, I need an A in Maths and just a pass in Further Maths..
The modules are interchangable, but who gets to choose!
Obviously I need all the best scores to go into normal Maths, but could college average them both out so I get like two B's?
If they did, I will definitely fail my offer.

Generally, the exam board prioritises Maths over Further Maths, so actually AC is more common than BB.

I think I'm cutting it fine as it is, I'm expecting A in maths and E in further maths. Do you think they will keep it that way then?

what happens if you did 3 applied modules for the standard A Level Maths - do the best two applied modules count towards the final grade?

Yes. Assuming that you did Edexcel they'll count C1-C4 and then the two highest of your applied module grades