If the partner portion of the 401k contribution is recorded as a "guaranteed payment," which would be shown on line 10 of the 1065, then the employer contribution would go on box 18.
Since it is just you and your partner that are participants, you would file the 5500-EZ. I have attached the IRS instructions in case you have not read them.
As far as your final question, the deductions are already made on the 1065 via box 10 and box 18. If box 13 on k-1 generates from the said inputs then ok, but do not add it anywhere again.