Motorcycle Repair: CHANGING FLUIDS, oil drain plug, 2 quarts

Question
2003 SOFTAIL HERITAGE CLASSIC, EFI. 7500 miles, all service work done by dealership until today!
I was trying to change the engine oil, removed a drain plug on the bottom front & just a small amount of fluid came out, there is another drain plug near this one, I opened it, only a small amount of fluid came out. I eventually found the engine oil drain plug/bolt & changed the oil. My question is what are the 2 other drain plugs? They do not have a bolt type head like the oil plug/bolt, nor did they have an oring. I am thinking this may be the transmission drain(s). The owners manual shows the tranny drain plug to be like the engine oil type of plug oring & magnetic. I can not locate this plug as shown in the manual. I checked & rechecked the transmission fluid, it seems to be full. one other question: the engine oil only took 3 quarts manual calls for 3 1/2 quarts.  

Answer
the hex plug facing the front side of the oil tank is the engine drain plug, the transmission drain plug is on the right side of the oil tank and it faces Up towards the seat and looks just like the engine oil drain plug, The little plug you removed is a engine drain plug, You do not have to remove this one. the bike takes 3 and 1/2 with new oil filter. If it did not take it all thats is o.k. just do not over fill either one,   JOHNNY