If by Rosh Chodesh Nissan there was any money left which could not be used for the new karbanos, the money was used to make gold plates for the kodshei kodshim.

R’ Yishmael who holds in the previous mishna that the treasury could buy, sell and make a profit, says that the extra money from selling goes for olahs brought when the alter was empty. The left over that was not sold goes for the utensils of the Bais Hamikdash.

R’ Akiva says the left over money in the treasury is used for olahs brought when the alter was empty. The left over from the minchas and libations (this would occur if hekdesh brought in a lot at the beginning of the year) goes for the utensils of the Bais Hamikdash.

R Chaninah segan Hacohanim says the left over from the minchas and libations (this would occur if hekdesh brought in a lot at the beginning of the year) goes for olahs brought when the alter was empty. The left over in the treasury goes for the utensils of the Bais Hamikdash.

Shikalim 4:5

The left over from ketores, incense, was used to pay the workers of the Bais Hamikdash. This was done using the concept of lev bais din, which says that some of the shekalim that were given, relinquish their kedusha since people gave it on the condition that the cohanim will make the decisions. Then they redeem the amount of the worker’s wages on the ketores and give the ketores to the workers . Then they would buy back the ketores with the new years money and would be able to use it in the new year.

If the new money came in on time, they would buy it back with new money. Otherwise they could not buy it back and the worker would keep the Ketores.