As I can't really figure out from your description why this should be happening, I'm going to have to ask for more information.
Firstly, dual booting should just work (TM) with the major distros and an installed copy of Windows. My guess is that you are being asked a question and misunderstanding what you are being asked for, and things are going wrong from there.
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So I formatted the drive and installed Ubuntu it dueled booted just fine
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So, am I right in thinking that everything about Ubuntu was fine, except that it was Ubuntu and you wanted something else? Or, am I missing something that didn't work? If so, what exactly happened that you didn't like?
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I will try installing fedora with the replacing option during the install...Well low and behold it gave me the same error.
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Any chance of saying
exactly what that error was?
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what is the best linux out there
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Sorry, but no clear answer. Every Linux distro out there suits somebody or another, or some use case or another. I don't know which one suits you, but try a few Live CDs to get an idea of which it might be.
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how do you install programs on it from my research there are three different file extensions for programs.
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I am afraid that you are overcomplicating things; Linux distros (largely) have application installers; use the app installer, click on what you want and its installed. Not hard. It will automagically deal with getting the right version for your distro. It will automagically ensure that you get your software from an approved source. It will automagically ensure that you don't have to worrry about file extensions.
There are probably command line options for the distro that you select, but you don't want to start there, unless you want to show off, or do something to several programs at once.
OK, I don't like Fedora (historical reasons), but some people do. Probably the most frequently used 'starter' distro is Ubuntu and there is nothing terribly wrong with it, but you might also look at Mint or Simply Mepis, as 'quite like Ubuntu, but with a somewhat different slant' distros.