If you're going to be visiting multi-cities, want confirmed reservations and don't want to use a store-front travel agency, you're going to have to do some work to find reasonable accommodations.
If I know what hotel I want to stay in, then I'll check first with their website. Chains like Choice Hotels have properties in a wide range of styles and prices. So I'll check with them, if only to give me an idea of the price I have to beat. When we went to Birmingham, UK, this spring, I saved $15 a night by booking with Expedia rather than the Choice website. For our honeymoon on the Oregon Coast, I booked through the Inn at Spanish Head's website, and saved $85 a night. Sometimes I'll just do a search for accommodations in a certain city and see what comes up. Sometimes some little-known local booking agency comes up with terrific deals. I've used these a couple of times though I admit to being a little hesitant because I didn't know anything about the booking agency.
I'm also a big fan of the Motel 6 chain, having first stayed in one 40 years ago when the cost was $6 for a double. Motel 6 motels are good, basic accommodations, though sometimes the location isn't always convenient. When I had a dog, I always stayed there because they didn't hassle me about him -- he was as welcome as I was. I also like security features at check-in. Even if you're the only guest checking in, clerks never say your room number out loud, but point to it on the map, indicating how to find it. I once checked into a major chain hotel with a lobby full of other guests waiting to check in. In a loud tone of voice, the clerk announced my room number and told me where to find it. Not good, especially if you're a woman traveling by herself.
I've also used hotwire.com and priceline.com to find accommodations. The drawback with these is that you don't find out where you'll be staying until after your credit card has been charged. You can, however, select your price range and general location. I've used hotwire a couple of times for trips to Seattle. We've gotten a Marriott for $55 a night plus taxes; the Marriott website lists room rates starting at $169 for this particular property. I used priceline to find out hotel in London last spring. I was reading online reviews of properties in our price range, and, let me tell you, they weren't good: linens that hadn't been changed in six months, smelly rooms, bed bugs, filthy rooms, etc. Nothing I would stay in. In desperation, I turned to priceline.com, asking for a four-star in Kensington, figuring it had to be decent. I also bid $65 a night plus taxes. OK, so I was maybe dreaming a little bit, but guess what? The London Copthorne Tara accepted it! It was a wonderful hotel (pictured above) a three-minute walk from the High Street Kensington tube stop. The staff tried to sell us an upgrade when we checked in, but we held firm. The rate didn't include breakfast, but we were given discount coupons for breakfast. The breakfast wasn't that great for the price, so usually we went to a nearby McDonald's or tearoom. The Copthorne chain's website said rooms at the Tara started at $200, so we really lucked out.
You can also try negotiating directly with the hotel. Our trip to Beijing last fall was one of the few times I booked accommodations and airfare separately. Friends were going with us, so it would be two rooms for 12 nights. Because of this, I felt a discount was called for. The hotel gave us one night free for each room -- I probably should have held out for a larger discount, but it worked for us.
Also take advantages of business rates if you qualify, and AARP or AAA discounts if you belong to either of these groups. Properties will give discounts of 5 percent to 20 percent for these memberships. You will only get these discounts if you book directly with the property, however..