In the intro tutorials, it is made clear that it is best not to apply styles to body copy, as it can interfere with the export/compile process.
However, when I have begun typing in my document, the default body text (13pt. Palatino) doesn’t seem to have proper paragraph breaks: paragraph breaks have the same distance as line breaks. Why?!
My question is this: how can one adjust the default paragraph breaks for body copy without interfering with the compile/export functionality at the end?
You can change this in Preferences in the same place where you set default font and size. Simply use the Format menu command to change the space before/after each paragraph.
I tried doing this in the Format menu > Line and paragraph Spacing (changed the ‘After’ setting)
This change the selected paragraph, but did not change the default setting across my project. 
did I not change it in the correct location?
Do it when you are in Scrivener -> Preferences where you set up the deafult settings for the editor.
Ok, I’m in the Preferences, but I can’t find the option to change the space after for paragraphs,
I’ve looked through all of the menus – but cant find it.
Use the normal Format menu, like you did before. At least that’s the way I think I changed it…
Yeah, I tried doing it though the Format menu – it doesn’t seem to apply it to the whole project, though. 
It’s not retrospective: changes to the default paragraph style only apply for new documents.
Instead, select all the existing documents you want to update and then Documents > Convert > Test to Default Formatting…. You’ll be given a dialogue where you can set the parameters of the conversion.
The conversion can be ‘undone’ I think, but it’s probably best to make a backup copy of the entire project first. Also, it’s worth testing the effect on a single document within the project first. Ideally choose one where you’re using italics and bold and other styles (or just create a dummy one). The idea is that you get a feeling for what changes will be made before doing it for real — I’ve never had a problem with converting documents, but no harm in checking first.
HTH.
Aaaaaahhhhhh…that makes sense. Thank you.
I will try that out and report back. Merci! 
Yep, got it, thank you.