Please tell me what your Multiple Distribution screen entry is so I can reproduce the problem.Is the deposit made to your checking account at the bank and then the bank transfers it to your savings? Or at the time of deposit of one check, does the bank split the deposit immediately?
If the bank deposits the $1000 and then transfers the money to savings, then you need to do the same for audit purposes. Deposit the $1000 to checking, and then post another entry to move it to savings. This will invoke the transfer clearing account utility and post to both journals.
If the bank splits the deposit immediately, then you also need to make 2 separate entries, $750 to checking and $250 to savings in each respective journal. This will match your bank statements and then also provide entries in each journal for reconciliation capability.