I can speak from personal experience on this topic.  In 1997, I designed and built an Ipe deck at my father’s house around his pool.  This was a project house, and you can see from the first picture that the old deck and fence had to go.  The engineering challenge was to sink the deck flush with a new stone retaining wall around the pool and butt it up against the fence. 

My decision to screw and plug the face boards came after worrying about the severe Texas summers and the stress on the 4/4 x 6 face boards.  I also considered ease of replacement should I need to take a board out.  It seems a lot easer to be able to drill the plug and unscrew versus…well, I’m not even sure how to remove a board after a hidden fastener has been used.  Finally, in my personal opinion, plugging just flat looks better.  It was a learning process, and here’s what I figured out:

1. Practice screwing and plugging on a spare piece before you actually start!
2. Set the depth of your countersink pre-drill hole with masking tape on the bit.  Make sure it is deep enough to receive most of the plug, but not shallow enough that the plug can’t grip inside the hole.
3. Make sure that you have an extra countersink bit handy, in case you break off your bit (I learned this the hard way).  Ipe is DENSE, and the bit gets hot quickly.  Keep some water or cutting oil handy, and frequently dip the bit to keep it cool.  Be careful with cutting oil – don’t get any on the deck as it will stain Ipe (yes, I learned this the hard way too!).
4. Set your pre-drilled hole about 1″ to 3/4″ from the edge of the board, or as close as you can get it based on your plug size and still maintain a nice aesthetic.  This will help to prevent any potential cupping of thinner material.
5. Pre-drill one hole, then immediately set the screw.  It helps if you have two drills handy, one with a countersink bit and one with the driver bit, so you don’t have to keep changing bits.
6. Make sure you are using stainless steel screws!  I like to use a small head, Swan Secure Woodpecker #7, with a square drive (they don’t strip).  Swan Secure is a good brand.  My experience with the “Home Depot” wide-head #8 stainless steel is that the heads break off frequently, even with pre-drilling.
7. Get a Bo-Wrench!  This little jewel will save you lots of pain if you are working with long or slightly bowed boards.  It clamps to the joist and jacks your board into it’s proper position, holding it there for you to set your next screw.
8. Use a long guide to gap your boards.  I used a 1/8″ plywood scrap and it worked great.  Ipe shrinks and swells with heat, humidity, and cold.  Proper spacing will prevent the boards from buckling or popping.
9. After you have face screwed all of your deck face boards, it’s now time to plug.  I found out real fast that Gorilla glue was not the correct glue.  It will also stain your deck.  A little dab of Tight Bond (#3 for outdoor, I believe) is what I ended up using…a little dab around the bottom is all you need.  Too much glue will force up the excess when you press down, and you will have a mess.
10. Tap the plug with a mallet as far as it will go.  TAP it, don’t hammer it.
11. Once all of the plugs are in place, I recommend making a few passes with an electric hand planer.  While this is an extra step, it will save you time in the long run.  Plane each plug to where it is not quite flush with the deck face.  If you don’t have access to a hand planer, a second method is to use a sharp chisel, turned on its beveled angle and make sure you tap the chisel with the grain. 
12. Go back with a belt sander to finish smooth.  It’s up to you whether you want to sand the whole deck.  I did not do that, as it was already smooth by East Teak’s millwork and did not require further sanding.  The second photo shows what the plugs look like after they have been set, planed, sanded, and the deck face finished.

I’ll leave the finish for another blog post for another day, but here’s a picture of the finished deck!  Not bad for an amateur.  If you have any quesions on your project, you can reach me in my office direct at (972) 248-0078 any time during the week and I’d be happy to discuss this process with you.  If there are any professionals out there that can lend some advice or if you have a better method, please comment!