Trip advice and expertise needed for first time in Czech

I am planning a trip with my girlfriend to Prague from Boston and my plan is to spend a few days in there and then possibly take a train to Amsterdam then fly back to Boston after another couple of days. My flights seem to be somewhere in the range of $1000 USD for each of us and I am trying to organize a very fun trip within an affordable budget. I have no idea on where to stay and what to do yet. I am happy to hear some advice from those in the know. We want nice clean accommodations but do not want to spend too much $$$ as we are only really planning to sleep in our hotel and spend the time exploring this beautiful city.

If you click onn the hotel link at the top of the page you will get a variety of options.
I would stay in the Old Town area, lots of options for hotels at reasonable prices but if you are prepared to stay in areas Like,Smichov,Devicka,Zizkov and Vinohrady you will get much more bang for your buck.Prague has a great cheap public transport system so staying out of the city center is not a major problem
have a look at what is available and in your price range,make a shortlist and I can try and advise you of the area ,transport etc.
http://www.prague.net/useful-info
this website will give you lots of info on what to see and do.

Hi, Demfer, I'm also organising my first travel to the Czech Republic and I'm reading all the posts for they can be a very useful guide. I've found lots of things to do and see in Prague, not all of them cheap, but some of them will not endager your wallet's health. Of course, it depends on your idea of "funny" and "inexpensive", but from my personal list I suggest you a visit to Prague Zoo (ranked 7th in the world) and some non verbal theatre as the Laterna Magika. I saw them in Buenos Aires many years ago, and they were fantastic. And very "Praguish" as my Czech mother says). Here you have a link to explore.

http://www.laterna.cz/en/

Near Charles Bridge there is Kampa Island, that looks both beautiful and interesting. In case you like live jazz bands, there is the Jazz Dock Club in Kampa:

http://www.jazzdock.cz/en/programme/?91322128.

My list is longer and still under development as I am going to stay some 10 days in Prague, but roaming along the city 'till my feet cry for a rest in an old style cafe, is item No 1 in it, and I think it's the best way to discover the city by yourself and selecting your own favourite places there.
I wish you'll enjoy your trip very much wherever you go and whatever you do.

Hi Demfer, I'd try to stay in the Stare Mesto or the Nove Mesto as these central areas are real
close to about 90 percent of Prague's great sights. Even with the metro and trolleys Prague
has, you two will be walking-- a lot. And having your lodgings handy to the sights means
you will be saving time ( and avoiding a few foot blisters) and can easily do Prague The "Hotels" link
at the top of this page lists several hostels in these two neighborhoods.

Demfer- Unless taking the train from Prague was something you really wanted to do- it's probably
going to be a lot less expensive flying between Prague and Amsterdam. I just checked kayak.com
and Easyjet had a summer flight for $96 RETURN between the two cities. Most other airlines are
around $200. The trains fare will easily top these prices.

A day trip out of Prague could be to Kutna Hora, which is 1 hr by train outside of Prague if I remember correctly. One of the major attractions there is an interesting bone ossuary ("Bone church"), where they've artistically arranged the bones of thousands of people who died during the Black Death into decorations.