I did mine a few weeks ago, but I'm pretty sure you can go back to edit the first part of the application once you progress to the upload section, yes. Until you submit the whole thing, you should be able to edit your responses. I would love it if someone who is 100% certain can respond though!
There is a placeholder for a LOE, or you can include LOEs with the documents in the relevant section - just merge them into the PDF. I've seen some people upload a separate LOE that covers everything, and others with individual LOEs for particular sections.
As far as I am aware, if you don't pay all the fees up front, you can only pay the additional ones when requested to do so, but - again - someone with better knowledge should be able to help here. I paid mine upfront, so I'm not sure.
Sorry my response is only partly helpful!