I think the cause of the confusion could be eliminated by moving the phrase "as a project director in Ecuador and in Mexico," to the beginning of the sentence (deleting the "in" before "Mexico," where it is unnecessary), and changing the "from" to "by," so that it would read as follows:

"As a project director in Ecuador and Mexico, I gained expertise in effective communication by negotiating in professional settings, meeting with my staff, and presenting to volunteers."