Developing a long term landscape master plan would be applying your needs and desires to the existing conditions. Existing conditions would also include what is outside of your yard -- good and bad views, shade cast into your yard, grade issues, etc. Based on the drawing above, we barely understand any of these things. In order to answer any question like if you should replace the green circle with a pear tree, we'd need more information, since we can't see what's there now.

Since you already have much of the basic information from the satellite view, I'd move ahead and create a base plan, with the goal of having it be as simple and readable as possible ... just lines on a white background, showing only permanent features that will be retained. You'll use copies of it to doodle ideas on and to create the finished master plan. So you don't want to show anything extra at this point. It's good to know where the septic system is, but it won't show as a major feature of the finished landscape master plan. Instead, the elements that you create over it will show. For the base plan I usually show only the trunks of individual trees but not the canopies, in an effort to keep the drawing simple. (The trunk let's me know there's a canopy there and I'll see it in the pictures. If the tree remains to the end, the canopy will show in the final drawing.) Show the canopy edges of wooded areas. Here's an example. (You would need to make it accurate if you were going to use it. I'm guessing at a lot of stuff. Ignore the green lines and blue dots.):

It's best to limit the discussion to one area at a time in order to keep it from becoming confusing. To get feedback and help, you'd need to make the site understandable through photos, which are best done as wide, complete scenes. Many shots of different areas from different points of view are hard to understand and sometimes almost useless. It's better to stand at a single location central to the scene and begin taking a series of slightly overlapping photographs than pan from far left to far right. (A computer generated panorama does not work because it is too small, without detail, and is distorted.) The blue dots are suggestion of some locations you might likely take photos from. Some photos would be inward (toward the house) if foundation planting is the subject. Other photos would be outward if views and perimeter plantings are the subjects. Add photos of a given area as you bring it up for discussion.

I would think a septic drain field is buried deep enough that you could grow minor plants over it, the same way that grass is growing over it. It doesn't seem that you would be limited to keeping the raised vegetable boxes in their present location .... not if it's going to limit something of greater importance.

My only thought, given the lack of information, would be to not do anything irreversible for one full year. See how you live in the space. See what pops up in different seasons. Where do you tend to walk, sit or work? Where do shadows fall year round? Where are the micro climates? Are there frost spots? Or wet spots? Where is the best soil?

Hire a consultant or designer to view the site in person, discuss your objectives with you and help you see how to make them happen. One way to line somebody up would be to click on FIND PROFESSIONALS at the top of the page here.