doggy,
I can't stress enough that you MUST get a firm handle on Vnav. Learn what it will do and when, as well as what it will not do. In my outfit it seems that Vnav causes the most confusion.
As far as fuel panel set up goes, SOP will sort it and does it really matter what happens when flaps are extended to a take off position? With a tank to engine set up for T/O you won't be very heavy so 1 boost pump out is not a biggy.
BTW, I came to the B744 after 21 years on B747 classic. Never forget that the B744 is EICAS driven. Wait for a message with very few exceptions.