My experience of crossing the Ecuador/Colombia border is from mid 2016. I rode N/S and S/N a couple of times as I had to have bike maintenance work done in the other country.
The main border on the Panamericana has 100s of cars crossing N/S and S/N every day. Mainly Ecuadorians and Colombians travelling for leisure or business. There are no formal barriers, nor anyone checking if you have correctly completed the formalities before allowing you to leave.
Assuming you're not planning on returning to Ecuador with the bike, I'd suggest parking up on the Ecuadorian side, doing immigration and then hopping back on and riding to the Colombian side and doing immigration/customs.
On the Ecuadorian side, I had to ask where customs was, as in the disorganised chaos and masses of people that exist, it wasn't clear. Their building certainly isn't signposted.
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