Ok, in short, my students write four papers short papers (8 paragraphs each) throughout the term then finally pull it together at the end as a final project. Each of the four have to be handed in twice about 2 - 3 weeks apart. The first of each is about 1/2 done or could be a draft and the second of each is a final version of that one paper.
As far as Moodle goes, it is rather simple. Set up various times when each segment is due and they submit accordingly. Having to show progress minimizes plagiarism and prevents garbage from being handed in all at the last minute. OTOH, evaluating the projects can quickly become a nightmare. For me it is 44 students times 17 submissions makes for about 748 short papers to grade.
This becomes a series of assignments spread throughout the semester. I restrict it to one paper being submitted at a time and a clear definite deadline for each.
I would restrict deletion so you can keep a history. Set up for multiple hand-ins to allow revisions before the due date and grade only the final version. In your spare time (-: you can review early submissions for improvements and hand them back though Moodle.
You should also download all files on the due date/time and keep an archive.
I cannot think of much else for Moodle and that may be as far as it should go here. If you want more discussion about the task and policies, I have been working jointly with another instructor and he has it all on his website. Originally it was his concept and I streamlined it in Moodle.
Maybe you might contact me directly as it will soon, if not already, be off-topic for a Moodle Forum.
Gary