Do you mean you want to hire a car for the return journey? if so I think you will find it very expensive, some car hire firms don't want the car taken abroad especially to the UK where the steering wheel will be on the wrong side and you would have a large one way drop off fee to contend with, plus ferry fees. and it's one very long drive.
If you mean you want to get a coach back there is an outfit called(I think) the Europa Bus which I believe is conected to National Express and of course you can get a train all the way back.
To visit Salzburg and Vienna I think your best bet would be find out to which city you could get the cheapest flight and after a few days get the train to the other city, it takes about three hours. You really don't need a car in either of the cities. In Vienna you can catch the underground and Salzburg is small enough to walk round and if you want to visit places out of Salzburg the public transport is pretty good.
I usually book hotels on http://www.booking.com or http://www.venere.com

thanks ,i think we will fly there and back and find our way around on public transport, just not sure where to base ourselves vienna or salzburg as we want to see both, x

You might like to contact the Tourist Offices in each city and see if they offer a 'Card' which will offer free unlimited use of public transport within each city and reductions on entrance fees to museums etc.

There are good train connections between Vienna and Salzburg. For good train details I would suggest you look at Deutschebahn's web site (which does all over Europe!) (http://www.db.de) and then book your actual tickets when you get to Austria itself.

Austrian Railway's passenger division website in English is at http://www.oebb.at/pv/en/ and you can check schedules and fares. The standard single fare from Vienna to Salzburg is €44.20 but if 2 people travel together there is about a 10% discount, the system automatically applies it as long as you ask for 2. Online tickets can be printed directly so you don't have to worry about them being posted.

Depending on where you start it may be cheaper to look for flights to Bratislava (Slovakia) which is actually Vienna's second airport and served by direct coach links. There aren't many cheap flights into Vienna especially if you want to come back from Salzburg. There are cheap flights from Salzburg, especailly as you will still be in the ski season.

Hotels in both cities are expensive compared to the Austrian average but it is possible to get better value if you stay in the surrounding country area, especially in Salzburg where a 15 minute train ride can make a huge difference.