When you have your philosophy and your style of play dialed in, and put in sufficient work evaluating your players, putting them into positions comes naturally. You can see the qualities they have, and how they can be leveraged the best. You'll know if a player who is good in 1v1s and a good crosser is a better fit as an outside back or winger. Or if a player that can read the game defensively and pass is a holding mid or a center back.
I've found the players that I have trouble pinning down to a single position usually fall in to one of two extremes: the best players on a team, and the newer players. The best players are good enough in a variety of areas relative to the team that they can contribute in multiple positions. In that case, it's usually a simple matter of slotting them into an area that they can have the biggest impact. I've found it usually means putting them into the middle of the field, usually as a center back, center mid, or striker. If that doesn't seem to be the best solution, slotting them in to a problem area, and replacing a weaker player, is another option.
The newer players are more difficult. High and wide is usually a good bet. They can contribute offensively just by staying out wide and stretching the other team, and defensively if they get beat it won't cause as many problems if they're in a deeper or more central position. It's simpler to work on their positioning, and they can contribute by being taught to make good decisions off the ball.
I've found that if I can't find a position for a player, and they don't fit into one of these two categories, it's my fault as the coach. Either I don't have enough experience with scouting players, I haven't dialed in exactly what I want from each position, or I'm not paying enough attention when evaluating this particular player.