I would like to go to Entebbe Airport but make a stop of say 2 weeks in Logos. Will my luggage be flown to my final destination?
You'd ordinarily need to specify the airline and other details (single ticket vs multiple bookings, etc....), but in this case, it's pretty unlikely that any major airline will hold your luggage for you for two weeks in this situation. Airlines are not in the storage business.
Your luggage will be flown to your stopover point, where you'll need to claim it. You can then take it with you or arrange for someone to store it (this may be available at the airport; is "Logos" really "Lagos?") until you check it in for your next flight.
I have done what the OP is trying to do, though I was transiting Kuala Lumpur and my stopover was only 29 hours, also I specifically asked the check-in staff to check my bag through to my final destination. I presume my baggage just sat around the baggage handling area until the connecting flight was ready.
I have also had an occasion when I stopped in Los Angeles for 6 days but on that occasion I had to pick up the baggage and use a storage service that advertised at the airport.
I guess it will depend on the country and airline in question. Best bet would be to ask the airline, probably the most knowledgeable person to ask would be the check-in staff or baggage handlers of your airline. If not ask them if there is a good storage service near the airport.