If you find that the new floor will look a lot better laid parallel to the joists (for instance down a hall instead of cross ways), use thicker plywood subfloor, about 1 1/4″ or simply two layers of 5/8″, as a subfloor. In this case you can still screw the occasional long plank to a makeshift joist. Counter bore and drill the holes in the hardwood where you want them. Now install a 2 by 6 bridge between the joist from down below, just where the screws start to come out. Then you can screw the plank into that solidly nailed 2 by 6, acting just like a joist.
It’s best to use a counter bore and pilot hole drill combination bit. Use a drill guide to keep your pre boring perpendicular to the wood surface. Better yet simply go to www.leevalley.com, and order their drilling kit. It contains all the drill bits you could possibly need for this task, and most importantly the kit also contains two plug cutters. Instead of looking around for the same species of wood for your plugs, cut your own on a drill press or a drill guide. Or you can also use a contrasting wood species like walnut. You will want to use at least 2″ screws on all the ends, and 3″ screws only on really wide plank floor where they intersect the joist. The size of screws you use depends on the bore hole. Two modest 3/8” to 1/2″ plugged holes would look fine on 4-6″ Planks. But you should use a 3/4″ bore hole on 8-12″ Planks. Once the plank goes over 8″ you will be using 3 screws in all the ends and long boards. Generally the screw sizes will range from #10-#14, they just have to match your counter bore unit. Oh, I almost forgot, don’t do the ends where they meet the wall, this will look silly, unless they are completely cover by the molding.
I have found that the best screws are the German made Spax screws, available at Lee Valley tools. They have a thread design that allows for the very smallest pre drill hole to be made. The design of the screw itself then cuts it own threads and holds almost like a machine screw. Very effective, and worth the extra cost. Don’t use drywall screws here, they are brittle and will snap off in time.
The pegs will get glued into the bore holes by a good PVA carpenters glue. If you have used the Snug Plugs provided by the Lee Valley drill kit your plugs will have seated in without a visible glue line. Only when the plugs have dried overnight should you cut them flush with the floor, with a special flush cutting saw. You can see why this method won’t work well with a prefinished or presanded plank floor. The surface of the wood will be so marred with all this screwing and pegging that the floor logically will have to be sanded and finished on site. But there is a way to end fasten these types of floor, without using screws at all.