I want to ask my manager something. i tried this
I have some questions, though I do know that I have asked you a lot and I am so sorry for losing your time.
is though correct in this context?
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If you really wish to use the word though in that location in that sentence, you should prefix it with "even" to make the sentence flow better.
I have some questions, even though I do know that I have asked you a lot and I am so sorry for losing your time.
However, the best way would be to rearrange the sentence.
I know I may have asked you a lot of questions, and I hope I am not wasting your time, but I have some other questions to ask you, if that is okay.