There are four main ways to travel throughout Scotland: by car, bus, train, and by ferry.
For car hire I use Auto Europe, a car rental comparison site (similar to Skyscanner). I have my own car in Scotland, however, I used Auto Europe to hire a car on my recent trip to Ireland and they were fantastic. I was able to secure a great rate that included insurance, so all I had to do was pick up my car from the airport when I arrived.
Travel by train is my second favourite way to get around Scotland.
Scotrail is the main railway in Scotland. Their website is very useful for researching train routes and prices.
For travel within the UK, I recommend first looking at Megabus. They have some fantastic fares- some for just £1!
Stagecoach is another popular bus company in Scotland.