There's enough above to answer your question, the lowered bike doesn't matter enough to affect things IMHO. Don't simply pour a set quantity of oil into your bike, use the dipstick - that's what it's there for! Stop when you get to a suitable level, whether that is a little less or a little more than 3.5 quarts.

 

Like GR said, it will make no difference. My bike is lowered all over the place and it has made zero difference on the oil level on the stand. By the way, I usually check mine on the jack as that's how I store it in the garage. It really isn't anything to worry about.

 

So I drained all 3 holes and left them to drained over night and until after work the next day. Put the 3.5qts of oil and when I checked it hot it was just over the bottom line I added another 1/4 qt so 3 3/4 qts in all. checked it cold and it was in between the lines and almost full when hot. Thanks to everyone for the post!