From $9ers site:

For example, Kyle Williams suffered a football-related injury to his ACL in New Orleans. He, as one example, will likely begin the training camp on the Active PUP. Once he receives full clearance from the 49ers medical staff, he is eligible to practice. Although he showed a "green light" icon on his Twitter and Instagram accounts, he has only been performing individual drills. He is yet to actually practice with the team.

Another player who is likely to start on this list is Kendall Hunter. He suffered a season-ending Achilles injury on the same play that injured Williams, and performed individual drills in front of the 49ers medical staff. He too, is awaiting clearance to practice with the team.

Second, there's the Reserve/PUP (regular season PUP list). Any player starting on the Active PUP list (and has not practiced) with the team becomes eligible for the Reserve/PUP. Once a player practices during training camp, all PUP list options are off the table. This is important to note. Both Williams and Hunter could be cleared within a day or two of the start of training camp, but starting them on the PUP list leaves it on the table as an option if there is a setback.

If, during the season, a player sustains injury but practiced at camp, the PUP list is not an option. The team can keep the player on the roster, if they believe he will come back that season. But, the injured player is counted against the 53-man roster.

In the alternative, teams must go straight to the Injured Reserve list (lose the player for the remainder of the season) or waive the player. So, it means the 49ers are extremely cautious about letting any player practice, no matter how good he looks following an injury. As you can see, letting a player practice makes the difference. Allowing a player to "practice" limits options. It can tie up roster spots and, more importantly, dollars.

It should be noted, ALL player salaries of a team count in calculating that team's total salary cap during the season. This includes players that are on Injured Reserve (IR), Physically Unable to Perform (PUP), and the Practice Squad (PS).

If a player started on the Active/PUP list and isn't medically cleared by the end of the preseason, the 49ers may transfer any Active/PUP player to the Reserve/PUP.

These players are prevented from playing and practicing during the first six weeks of the season. What makes the Reserve PUP advantageous is that any player on the Reserve PUP list does not count against the 53-man roster. If a player isn't activated after the sixth week, the team has a three-week window to make a decision to: 1.) place the player on injured reserve; 2.) release the player; or 3.) get him back to practice. As soon as the player returns to practice, the team has another three-week window to add the player back to the 53-man roster, or place them on the Injured Reserve list.

For example, Mario Manningham is a good candidate to see the Reserve/PU