Extension Number is the 2-digit number that you dial on Intercom to reach that particular phone. If you go to a phone (with a display) and press Feature 00, the display will say "Program Extension XX", the XX is the extension number of the phone.
Line Number is the 2-digit number of the line port that the telephone line from the outside world is plugged into. The 1st line jack on the ACS is 01, the 2nd one is 02, etc. The last line jack on the ACS R7 is 05, then you move to the card in the left-most slot, and that starts with 06
You do your programming from Ext. 10 or 11 only.
So, your phone is Ext. 23 (example), it already has lines 1 through 4, and you want to add line 5 and 6.
At Ext. 10 or 11, you press Feature 00, Left Intercom twice. #310-23-05-1 (add Line 5 to Ext. 23), then #310-23-06-1 (add line 6 to Ext. 23). Line 5 comes up on the button above Line 1, and Line 6 comes up on the button above Line 2 (assuming that Ext. 23 is an 18 button telephone).