So would there be any indication there was flash like would there be a popup asking them if they want to allow this flash object to run?
Don't think so, flash can even be used for some very sneaky operations (like cookie-stuffing) without any problems.
[offtopic] But it's limited to one site's cookie if I'm not mistaken? If you use .htaccess with an image?
Nope, you can basically forward the headers of a url to the browser (which may include cookies) so it gets stuffed. Kinda like someone stuffing a visitor's cookies with amazon and ebay cookies simply from viewing an image that's really a php file.
Flash and Java are pretty equal on blendability. Both have methods to create your own interface pieces. The first thing you'll want to do is determine how many of your visitors have either enabled. I have a mobile site for instance, with 41% of visitors not having Java enabled and 34% of visitors without a Flash version being defined. I've got another non-mobile site with 26% not having Java and 14% not having Flash. On a third site I have 1% without Flash and 11% without Java. As you can see the numbers can vary wildly. I use Google Analytics to determine these numbers. Another thing to consider, is the ease of installation issue. Installing Flash Player is almost idiot proof, where as installing Java usually gives people headaches. Java is more powerfull than Flash, in fact Flex uses Java to compile the bytecode for SWF files, but for an end user Flash is probably going to be your better option, in my opinion.
Can I just make it upload normally if they don't have Flash installed? Also can someone help me make this Flash thing? And will I have to make my whole upload script out of Flash now?
Use swfobject to include the flash file, with swfobject you can have the normal upload dialog in a div, but if javascript kicks in and they have flash it will replace that div with the flash method upon load of the page. http://code.google.com/p/swfobject/
Just use http://swfupload.org/ (there are code samples on the site) Alternatively, http://digitarald.de/project/fancyupload/