Thurs and Saturdays are the busiest days in Faro airport. Its when all the tour operators change over as well. Personally having been in the airport on both days i would try to avoid it, but if its the only days apartments will change over then you will have to go for it. Dont worry about booking flights there are so many apartments to choose from you wont have a problem booking accomodation. Although as your going in August dont leave it to long to choose.

Having done many DIY trips maybe I could tell you the way id go about it.
Seeing that you are planning to go in Aug,a very busy time wherever you go.Id do my sums and look at whats available on your chosen week/s first, seeing that you are going on a Fri I assume youve got a date in mind.e-mail or phone as many places now! (Dont forget tour operators block book all the main hotels all the summer weeks).Having secured your accom then Id book the flight immediatly after.Good luck.