During the install process you are able to select which drive you install to, any other drives are not touched. of course this does mean it's down to you to select the correct drive (I've selected the wrong one once! OPPS)
if you disconnect the D drive obviously the danger of selecting the wrong drive is removed. but are you sure you actually have two physically separate drives in the computer, a lot of computers are supplied with one physical drive but that one drive is split into two partitions that then show as two separate drive letters in "my computer"