I've been able to save a bunch of money by doing a bit of legwork. I cross-check all of the flights at the following places, and then I do the same for hotels. If you are comfortable with priceline.com you can find some great deals on hotels (I tend to like nice places, so I'd rather pay a bit more to stay at a NICE place using PL, instead of a crappy place using something like hotels.com) The 'combo' deals SOMETIMES save you money, but you should shop around because many times you only get a decent rate on the hotel room.
I think the APA 'deals' are just a way for them to make a bit of referral money, as you may get a slight savings, but it is usually no different pricing on your end, they just happen to get a % cut or flat referral fee for your booking.
Worthwhile Websites
www.expedia.com (where I start to see what flights go where, though I usually don't book through them because of their penalty charges for changing a flight, etc)
www.qixo.com (only for plane flights)
www.travelworm.com (good for hotel+flight deals)
www.travelaxe.com (I haven't used lately, though I think they have a stand alone application now to track deals. I use it for hotel pricing)
www.hotwire.com,
www.hotels.com, etc are all hit and miss and generally have the same exact pricing as other places. Make sure to check each site's re-booking charges as they vary. I use to travel a lot and most 'deals' on airline tickets come from using
Hidden City Fares, smaller carriers, last second flights, or major hubs for an airline.
www.priceline.com (worth a shot if you know what you are doing)
www.biddingfortravel.com (GREAT site to use in conjunction with PL, but Sheryl (the owner) can be...'particular', so read the posting rules if you are looking for help)
----
Airlines offer better pricing if you fly on off days like Mon, Tues, etc. You'll need to manually check places like southwest, spirit air,Jet Blue, etc. If you know what carriers go from your home airport, it really can help you get an idea of your options.
Staying with friends obviously saves money.
You can often accrue free nights if you stay at the same family of hotels, so if you travel around the US a lot, it is best to stick with one brand (Marriott, etc) as you will accrue free rooms quicker.