There are two outlet lines (ports or holes) from the pool to the pump for legal reasons. Two outlets splits the suction of each port in half. That makes it less likely that a young child could be held below the water line. Regardless..
Your pool kit came with a plunger valve that the two hose lines from the pool connect to. It's called a split plunger valve. Then from that connection, out from the bottom of the split plunger valve, one single hose goes to the pump. Just like in the diagram.
The black plug/cap you're talking about comes with your pool kit and goes on the inside of the pool on one of strainers on one of the suction lines. Then only one of the outlet ports actually sucks water from the pool, through the plunger valve and to the pump. There really isn't much difference in how water is circulated, regardless of the size of your pump whether there are two suction lines or one. (Except of course, the relative safety it provides by splitting the pumps suction between two hose lines in the pool instead of a single suction line.)
Having the suction split into two hoses at the pool affects your ability to vacuum efficiently. Or, if you attach a skimmer and have two outlets the skimmer will be less efficient.
The two hoses from the pool, to the plunger valve, to the pump work the same as one line from the pool to the pump.
If your not going to use the two suction lines and the hoses at all and you're going to cut in a through wall skimmer, then, the black plugs/caps need to be used to plug the two small suction lines.
May an amateur pool owner make a suggestion? Maybe you could set it up as the instructions say, make sure everything works, see what the two suction lines do, and then make any plumbing changes you want sometime after that? It seems it's not that difficult to make changes while the pool has water in it....
