I have(am) applied(ying) for a junior faculty position (i.e. tenure track assistant professor level) at a research-intensive US university from this fall. I am planning to apply to at least 30 universities for getting a position. However, most of the opening announcements I came across are asking to put the email addresses of my referees for letters of recommendation in addition to submitting standard documents, e.g. CV, cover letter, research and teaching statements. My concern is if I apply for all of these openings within a week or so, my referees' email inbox will be full of reference requests. In order to avoid such problem, I am applying for one particular opening and then waiting until I see that all the referees have uploaded their letters. Then I am applying to the next. However, it turns out not to be the best way of handling this circumstance since most of the referees are taking at least a week or so to upload their letters (sometimes after my second reminder). If it goes on this way, I will be approaching the submission deadlines of some of the openings. In this case, should I upload the standard documents from my side at least? Will the department I am applying to not consider my application if they see that the reference letters are not uploaded on time?
My experience comes with asking for recommendation letters with my PhD application, most of the times it was necessary to remind the referees about the deadline for submission; they're so busy that they easily forget about it.
Another option would be with resending notifications through the recommendation system; many of such systems allow for sending automated reminders to the referees thus eliminating the need for direct intervention with the busy professors!