I used to use the inline method, but switched some time ago to tying the second fly to the eye of the first. I like the thought that this might remove a little bit of encumbrance from the hook of the first fly and perhaps give it a little more of a horizontal orientation. I use tippet for that last fly that's one size lighter than the tippet to the first fly, with the reasoning being that if the bottom fly hangs up on the bottom and I have to break off, the lighter tippet should give first and let me have a better chance of getting at least the top fly back.