I log paper check payments to “undeposited funds” and then when I view transactions, I match those payments to the deposit. Should I also be entering the lump sum deposit
It is your choice. You would have to manually createtge deposit in QB prior to matching. Once you have matched to the bank feed as you are now there are no longer items for this deposit to create it again.
What you do now enters the correct deposit with correct payments but if you had a large batch over several days it might save you time to "make" the deposit in QB contemporaneously with making the deposit at the bank.
While I can see the benefits and have used bank feeds I am still a firm believer in doing the work first - then the matching is just checking up