Banking

When I pay our vendor bills, how to apply this to the correct bill as there are many bills with the exact same amount, even from the same vendor?

Also, what do I do with the banking section after I pay the bills? Meaning once the payment has posted to the bank and it shows up in Quickbooks. Will it automatically apply to what I have entered? Even if the amount due is the same amount? 

Thank you in advance, sorry if this does not make sense! :(