Seems to be some confusion over the term "permanent" bed. As I've used it in the past, it merely means that the bed is dedicated to alliums. Onions, garlic, whatever get grown in the same bed over and over again. The exact opposite of rotation planting. The idea of such permanent beds goes back to the 19th century, when commercial onion breeders discovered they actually get better productivity from using the same beds over and over again. The whole idea of crop rotation, as it turns out, has been greatly overplayed in almost all cases. There are only two reasons to rotate crops: Depletion of nutrients and soil-borne disease. In the average home garden, neither of these problems can be fixed by rotating crops. There just isn't enough room. However, assuming you replace the nutrients (that's what compost and other amendments are all about, people), and in the absence of a heavy infestation of a soil-borne disease, there is no reason not to grow onions, or garlic, or, to put a point on it, leeks, in the same bed over and over again.

Alyssa, Salvia is an excellent idea. Unfortunately we've got more than we know what to do with. However I don't think it is the same variation as you have. Usually it is very showy but it has struggled the last few years. I think something changed when cedar mulch was applied to the bed. We did not intend to mulch it because the plants always reseeded and did splendidly but there was a mix up with our gardeners and mulch was put in. I probably should have had it all pulled out but decided to see how it did. Since then they don't seem to be as good of bloomers, not as purple and not as showy. But it could just be they need fertilizer. We sort of ignore them other then to try and battle them back into the bed. You can see where they've been in the lawn and been cut out. This year there is something else mixed in. I don't know what it is. It looks about to flower so I guess I will find out. It is sort of salvia looking but the leaves are slightly different than whatever variation we have for most of the bed.

I like no-till gardening, but it is hard for me to make it work. I think what has worked best for me in the past was to grow a cover corp, which I needed for organic matter to improve the soil. Then, because my soil is nearly always too wet and too cold, ( I live in a low area ) I would mow the cover crop and start tilling, even though the soil was too wet. I had to get it bare to heat up and dry out. I know that is not good on the soil structure, but if I wanted to get a crop in before the weather got so hot that the tomatoes would not set fruit, I did not have a lot of choice. Another factor in my gardening method now is that I have become too old to till and get around well. It also take a lot of mulch, which I may not have access to. I like to use wood chips, but I don't always have wood chips. I think we all love gardening or we would not be doing it. Another thing we can agree on is that none of us have perfect conditions to work under. I would also say that we all like to experiment a little, which means, at times we will be doing things a little different, some work well, some don't, but the most important thing is to enjoy what you do.

I will leave it to others to answer your question of placement, since I’m unfamiliar with Japanese garden design. I would, however, think about one thing for your vegetable garden. Figure out how you are going to plant it so that each vegetable can be reached while you are stepping on something other than your planting soil. Vegetable gardens necessarily get more traffic than any flower gardens other than the most active cutting flower bed because you’ll be picking from them daily or close to it. Right now it looks like you will either have to step in your flower bed or in your carefully filled veggie bed to pick your tomatoes, water, or check for pests. One possibility is to incorporate some of your more attractive veggies in among the front of your flower bed, though I’m not sure how Japanese that is. The front of my flower bed has my salad greens tucked alongside shorter edible flowers. Another possibility is to make your veggie garden more of a U shape, with a path down the center so you can reach everything. Enjoy your garden!