Ne yaptığını biliyorum

it could mean ( i know what you are doing ) 

it could mean ( i know what you did )

it could mean 2 things, so how do you make a difference when somebody says like that?

Unfortunately you cannot understand.

If you want to be more clear when you speak, however, you can say "ne yapmış olduğunu biliyorum" to emphasize past.

Çok teşekkürler.