Never been to Portugal or used those providers so can't help you there RR. However, I rarely do whole package deals. I tend to book accommodation directly and arrange a cheap flight separately. As far as transport is concerned you can usually book a hire car to pick up and drop off at the airport. if you don't plan on using a hire car then Google airport transfers for the name of the airport and see what comes up. Last year we went to Menorca and for £25 the 3 of us had a minibus from the airport to the front door of our apartment. I paid in advance - they picked us up at the end of our stay as well. 

Having done that once I now know which bus runs out that way so if we went again I might just hop on the bus.  

Thanks Caraid!! Thats sound good, but the only thing I'd be worried about would be messing up something as its all done separately!