Coming from an academic background, when I type, I like to separate paragraphs with a double return and I don’t indent new paragraphs. I understand that this is not the way editors like manuscripts submitted. When I compile (or anytime else for that matter) can I get Scrivener to delete the blank lines and indent all the paragraphs?
During compile you can choose to override the formatting and so add indents. You can’t get rid of the extra blank lines that way, but you can do a project find/replace to delete them beforehand (or do the same sort of thing in another word processor with your compiled text). To do the replace, I’d recommend first backing up the project; then Edit>Find>Project Replace… Use opt-return in the fields to search/replace for the return character.
Note that the project replace will, naturally, replace this double-return throughout the entire project, not just in the draft, so if you want to keep it only in the draft use a regular find/replace instead with the entire draft selected and open in a Scrivenings session (and use “selected text” as the Replace All Scope).
Another option that may work for you in the future is to change your default formatting for this project (or for all projects, if you always work this way). In the editor formatting you can change the spacing between paragraphs to emulate a double-return. To do this for the specific project, go to Project>Text Preferences… and click the box to “override main text style,” then set the sample text to appear as you want it and click the line spacing dropdown (in the blue box below). Choose “Spacing…” and you can then set spacing for before or after a paragraph.
To set the formatting globally this way, you can set it in Scrivener>Preferences:Formatting.
Either of these will only affect new documents; you can use Documents>Convert>Formatting to Default Text Style to change any pre-existing ones (you can just select the bunch in the binder and then convert them all at once).
Sorry if I rehashed stuff you already knew. 
Just wanted to throw it out there for the sake of being thorough.
Thanks. That will help.