Vannakkam: Normally they're separated. You give the temple offerings as you enter ... the fruit and flowers, milk , etc. whatever you might have. Then later you sneak money into the hundi, and give the dakshina to priest. Because our temples in the wet encompass so very many Indian traditions under one roof, it's also a good idea to write 'Priest Dakshina on the outside of the envelope, especially when it's coming from you. He might think you simply don't know where the hundi is, or what its for, and error on the side of caution by putting it into the hundi.
Good luck with it. You can do no REAL wrong here, but I understand that you just want to follow the normal protocol. Not having visited that temple myself, I'm actually not that sure either, but I have been to enough temples to make a fairly educated guess. That temple is on my North American list.
Aum Namasivaya
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