Hi, welcome to BeoWorld!
Do you have Powerlink cables? You will need two.
You have two options here:
1) Wire each speaker directly to the BeoCenter.
2) Daisy-chain the two Pentas together and connect the Center to one of them.
Do not worry about which port corresponding to another port, they are all equal. Just plug and play!
You are correct, each speaker must be set to the appropriate channel, right or left. Once you have determined which speaker is which, simply set the L/R switch to the corresponding position of the speaker. Naturally, one will be left and the other right. The reason for this is due to the fact that each Powerlink cable carries both channels, so when you select L or R, you are effectively choosing which signal you want to hear.
Hopefully this is clear enough to get you moving. If not, get back to us!