Apologize for misunderstanding

You are well on the way. Since you ask I will add a few corrections.

To start I will say that you have Exchanged some emails with your boss. My basic advice is to say things as simply as you can. The more words you and your boss use the further they get from the goal.

I am sorry if I sounded as if I have problems with your advises [advice]

might be

I am sorry if I sounds like I have problems with your opinions.

or

I am sorry if it seems like I have problems with your opinions.

Best to make things in the present tense; I wanted by no means to sound like I have some sort of conflict with you.

might be

I do not want to sound like I have some sort of conflict with you. or

I would not want to sound like I have any conflict with you.