tandem flies

Let me start by saying hello. I've been a lurker here for a while and decided to join. My question is when you are using 2 flies, what knot do you use for the second fly. There is now way I could get a loop thru the eye of a size 14 or 16 hook. Thanks for any help.

I do mine just like this picture.  I use the Improved Clinch Knot at all three points (2 eyes of the flies and bend of the hook on upper fly).
 

On a very cold day, when my fingers quit working, I will reduce to two knots by leaving a long tail off the knot in the eye of the upper fly.
 
But, I prefer to use all three when possible.

When tying a palomar knot, don't try to push a loop through the hook eye.  Put the end of the line back through the eye and you'll have a loop.
 
For my two fly rigs I use a palomar knot for the first fly to the tippet, then a surgeon's knot at the bend of the first hook followed by another palomar knot for the second fly.
 
I've had so many failures with improved clinch knots, I've given up using them.

There are a bunch of ways to do it and they all depend on how you're fishing and how much effort you want to put into your rig.
 
The easiest is as described above, using a separate piece of tippet to connect the flies.  Tie in either at the eye, the bend, or onto the line above the point fly.  All have their benefits or problems as discussed above.  I probably use this method more than any other because it is quick to tie streamside.
 
Another option is to leave the tag end of your point fly knot long or use a palomar knot for the point fly.  If I'm doing it this way I'll always use a palomar since it is a symmetric knot- it doesn't matter which end of the line you pull on it is the same pressure- unlike a clinch style knot which makes a difference if you're pulling on the tag end or the running end.  I rarely use this method, about the only time I do is if I want to add a second fly above a fly I already have tied on.  Then you can double over the tippet and tie a palomar knot a few inches above the already tie on fly.
 
A more time consuming method but one that keeps tangles down is to tie the droppers into the leader.  Build your standard tapered leader to the first point of attaching tippet.  When you tie in the tippet, leave the tag end of the tapered leader long enough to tie on the point fly (about 6").  Then use the tippet to tie on the next fly.  Or, tie on another piece of tippet to the end of the first tippet.  Leave the tag long again like you did above for a middle fly and attach a third fly to the bottom piece of tippet.  The benefit of this method is reduced tangles.  Generally when you do it this way, the flies will stay separate so long as you don't leave the tag ends too long (i.e. don't let the fly go longer than the next tippet connection).  If you are fishing the same flies and covering a lot of water this method makes sense.  The lake fishermen over here do it this way because they are casting a lot all day and not changing up flies as much.  I like it for prospecting with czech nymphs.  The middle fly is the heavy fly (anchor) and isn't changed a whole lot once you get the right weight.  The top fly is normally a small light fly that you don't change much.  The bottom fly will get changed more, but it is on a longer piece of tippet (as opposed to the tag of a knot) so you get a few more fly changes out of it.
 
If you want to fish flies like this a lot, you can tie up a couple 3-fly rigs in advance with loop to loop conections and put a small loop on the end of your tapered leader (or just use a polyleader).  It is a great system and once you get the hang of it really easy to do.

Thanks,
Rick