I worked in a travel agency / global travel wholesaler.
Best advice I can give you is to NOT go through any travel agency or website.
Don't because:
1 - You'll be paying a BOATLOAD of money you shouldn't. The markup on most websites and travel agencies is well over 40%. That 1000 trip cost you 1400 because you went through an intermediary.
2- Its not guaranteed. Let me repeat that: ITS NOT GUARANTEED. All the legal snot you approve when purchasing the service from the website/agent pretty much gives them the right to tell you: sorry we fuked up, here's your money back, have fun being stranded in an unfamiliar place.
And you cannot argue with the hotel itself, you did not make the agreement with them.
All travel agents will secure the hotel room for you via a wholesaler/supplier. Those wholesaler/suppliers in turn either have a contract with the hotel or buy the room night for your agent... from another wholesaler.
As a bussiness, if the room you purchased in the hotel you selected is not available they will try and put you on the LEAST expensive alternative of equal or better star rating they can find. So that fancy 4 star intercontinental or hyatt hotel you booked is full, its the wholesaler's error.. they put you on the 'technically' 4 star La Quinta 10 miles away... the wholesaler just messed up your vacation, took your money and you cant do anything about it. And IF it comes down to the city being way overbooked (aka concert, event, etc) and theres NOTHING but a 5 star hotel costing 800 bucks a night the wholesaler will NOT place you there but lie to you that they cannot find any room and give you your money back and leave you stranded. Its policy.
My suggestion is to shop around and always buy direct from the source. It will not only be cheaper but also you have a valid guarantee (a hotel cannot leave you stranded)
Here's a few online tools you can use:
http://www.map24.com - map website. Shows hotels in the area. Much better than Google maps for this. Will give you the hotel's direct phone number.
http://www.hoteltravelindex.com - to check if a hotel is really a 1 or 5 star property. Not all hotels are here (of course) but its got the best 'list'. Use this only for non-chain/brand hotels (those you find their star rating on their websites and its trustworthy info).
http://www.kayak.com - search for cheapest avaible flights. Very good search engine. Use it to find the flight # and departure airport, etc.
then call the airline and buy it direct from airline. 
