Put them in Project64's Save folder. The name has to be the same as the rom's internal name. You can check the internal name by right-clickking the rom in Pj64's browser and choosing 'Rom information'.
If it doesn't work, you can use the SM64 save editor (search the board to find it) on a fresh eep save to get as far as you did on the cart. Obviously this will only work with SM64.