It is not exactly clear from your post what your itinerary is. I am assumuing it is the following:
- Fly into Bogota and spend 3 nights in Colombia
- Fly to Peru and spend X number of days/night sightseeing in Peru, including 2 full days in Lima
- Fly back to Bogota and spend 3 nights in Colombia before retunring home
If you already have two full days in Lima, I wouldn't spend any more time there. 3 nights and 2 full days in Bogota is about enough. I spent 6 full days in Columbia last may. 3 full days each in Bogota and Cartagena. To me, the two cities were very different. I really loved the very Spanish colonial but Caribbean feel of Cartagena. I wish I could have stayed longer. I love historical stuff, including museums. So I stayed in the La Candelaria area of Bogota. To me, the Gold Museum (Museo del Oro) was definitely the highlight of Bogota.