Sadly no, there is no way to save your "ammo" after playing the Song of Time...
HOWEVER!!!!! HERE is how you can make some easy cash:
1) There is a chest with 100 rupees on the roof of the Clocktown Archery Shop. To get there, go to the top of the Milk bar Past the Bomber who guards the entrance to the Observatory. Next you either need to roll and jump off the ledge, or apply the Bunny hood and run off the edge, twords the Honey and Darlings game shop. You should land on the baskets or the sign. Then continue to the roof of the Archery Shop.
2) There is a chest ith 100 rupees in the secret passage to the observatory. After you enter the passage sim to the left until you come across a platfrom with a cracked wall. Either apply the Blast Mask or use bombs to get to the chest.
3) In Termina field, next to the observatory is a tree with a man in it. Roll into the tree to nock down the man and and some Red Rupees. Take the Rupees.
4) This requires a Mask that changes your form and lets you roll around (no spoilers here!). Go into Termina field and go near the entrance to Milk rode. You should see a flying bird called the Takurri. DO NOT LET IT TOUCH YOU!!! Kill this annoying bird via arrows or Fire arrows. Collect the 200 rupees it drops, go into milk rode, go back and repeat until your wallet is full. Then tranform and roll back into Clocktown (hitting bushes to refill magic and arrows).
As for other ammo, they usually provide it when you need it. But If you REALLY want it:
1) Use the money you got to buy it at shops.
2) Go to Termina field and Spinattack Circles of Bushes (very effective)
3) As I said above. Many jars and blades of grass provide you with the ammo you need before each dungeon.
I hope this helped! CIAO!!!