From a recent discussion https://www.tripadvisor.com/ShowTopic-g294307-i2253-k13777965-Tips_for_making_transfer_from_GYE_to_Baltra-Ecuador.html

In January 2022, our friends planned an arrival into Guayaquil in the morning and was suppose to arrive 2 hours in advance of the 9 o'clock flight on Avianca into Baltra. They ended up missing the connection because of a delay on the first leg; and were able to get another Avianca flight a couple hours later.

When you arrive from US, you will need to go into customs; and then you have to go to the Galapagos booth for verification of paperwork (vaccines and covid test results and entry payment), then to the luggage section before checking in again. At least that was the process for us. Depending on how many people are on line, the lines can vary greatly.

I flew into Quito the night before and then checked into the airport for Galapagos in the morning and it took me about 30 minutes max but I checked in 2 hours in advance (which was probably not necessary).