1) I don't know what happens when you use the first two methods, since obviously I've never used them. Third method shouldn't produce the problem you reported. But third method has a different problem (because of an ongoing bug): the post may disappear instead of being published. So I would suggest you use the regular way: Posts > Add New (dashboard sidebar). In that case you can sidestep the issue you're experiencing in two ways: paste the Flickr code in the Text editor then continue writing the rest of the text in the Text editor, or write the text in the Visual editor first then switch to Text to add the code.
2) There are no div issues on your front page, and the sidebar is in place. Perhaps you're viewing the blog in a low resolution screen or mobile device. Confit is a responsive layout theme: the sidebar drops below the main content when the screen is too narrow.
3) "Only gives 3GB"? In my tests blog I have uploaded more than a thousand images so far, and they've only taken 8% of these 3GB. Just avoid uploading huge files straight out of your digital camera: use an image editing application (or an online tool) to downsize the images to the appropriate pixel dimensions, and upload these versions. Storage space apart, this will also mean faster loading and better quality.