Here's the answers:
# You can only set the plan as completed in the learning plan in user's profile. One way you can ease the navigation is to create the plans using "learning plan templates" at category level. By doing this, the manager (or other roles you may create) can easily view and go to all the user learning plans based on template from the category administration. Another possible navigation is when a plan or a competency is set to waiting for review, any user able to manage the plan of the student will see that a plan/competency is waiting for review on their Dashboard (learning plan block). Worst case scenario, the manager could still create is own HTML block with direct URL link to users learning plans.
# The evidence will be visible in the course and in the user learning plan. An evidence does not change the rating of the competency so no need to accept or deny it.
# First one will add an evidence and change status of competency to "waiting for review". When the second one is resolved, another evidence will be added and the competency will be rated with the default value defined in the framework. So it's more of a merging than an overwriting ;)
# No, you can, if you want, rate the competencies manually. You only have the specify "Do nothing" on course or activity completion when adding competencies and let the teacher do the evaluation.
# There's 2 levels of rating: In the user learning plan (from user profile) and in the course. If pushcourseratingstouserplan is true, when a rating occurs in course the value is pushed to the user learning plan. If false, the rating is only set in the course. Note that on every action related to evaluation on competencies an evidence is created so you can still see that a rating occurs in the course when you go see the competency in the user learning plan.
# Cross-referencing competencies do nothing more than showing competencies related to one another. I think the purpose is to make it easier for students who would build their own plan to find competencies to add.
If I'm not clear enough on some points, please let me know and I'll try to explain it better!