Your first question actually has several flavors. Course and
Lesson content (not
activities) can be uploaded in multiple formats. I would suggest reading the Moodle documentation. Here is a link to one for
uploading a course (it is for 3.5 as that is what I use). You can upload
SCORM packages, too. I have uploaded PPT files with limited success.
The Assignment activity (see 3.5 docs
here) allows you to let students upload any format or to limit to specified formats.
Your second question answer is, how detailed do you want to get. Teachers have access to the lesson's logs. Logs track actions often to the click level. However, to ensure step 1 is completed before step 2 is not difficult. First, however, your administrator must first turn on completion tracking. Without that, it is quite difficult. Assuming completion tracking is on, ensure Completion tracking is on for the lesson. When it is, all
activities and resources will have an Activity Completion section. In this section, you can determine if you want to track completion for that activity or not. If you do, you have several options, also
context sensitive. The first is, the student can check it off and say 'yep I'm done.' I rarely use this one. The next, automatically sets completion to true if the specified conditions are met. Students cannot manually check these off.
The content of the Activity completion section changes based on the activity and resource. By using this and the Restrict access (above the Activity completion section) together you can regulate to order of how the lesson flows.
In this case, topic 1 must be completed before continuing to topic 2. Here, I set the completion status for the first lesson to set it to complete once the student finishes the lesson. I restricted access to topic 2 until topic 1 is complete. Once complete, topic 2 is enabled since topic 1 is now complete.
If you want the student to say "I have read this", then add a one question quiz. The quiz is enabled once the reading is done. When the quiz is done, it enables the next reading. In most cases, this is going waaay overboard.
I hope this answers your questions.