Internal flights around Colombia are extremely cheap - I found generally not much more than a bus for long distances which can save you a 12-14 hour overnight bus ride. With 11 days, I would focus on either Panama or Colombia, you might have time to see a couple of big cities in both. But I had a much better time in the towns surrounding Cartegena and Bogota than in the towns themselves. I can't comment on Panama aside from the fact that Bocas Del Toro was incredible and well worth a trip (It is in the north of Panama so it will be difficult to see in a short time if you do come from Colombia).
I would recommend Cartagena over Bogota even fi you don't have time to escape the city aside from day trips. There is some beaches close by, and the city itself is really nice with cultural things to see and do. If you end up spending more time in the area, Santa Marta is a 4 hour bus ride away and from there, it is 1 hour to Tayrona which is a beautiful park.
In 11 days, you could probably get a feel for both countries and see some of the highlights, but I would try and pick one (as hard as it is), and focus more time there.