This may not help you, but this is how I organize plans:
Scrap paper-I sketch ideas out roughly as a thought process. I also jot notes here.
Local-I try to choose plants that I know thrive in my local, this cuts down on choices grandly, as every local has its peculiarities. I also look for techniques that work well in my climate or even harsher climates. Techniques that are wonderful for northern coastal california fail grandly sometimes in the higher, drier, winder, much more alkaline climate of the foothills of the colorado rockies.
Love it-If its something that doesn't appeal to me for any reason, it doesn't get to be in my garden. The only exceptions would be if its something my mom or dad adores to the point of wanting "that plant!" I also will find a way to grow it (within reason, as an urban gardener, there are space constraints), even if it takes years to find a variety or method that works. You would possibly be appalled at how many tomato varieties we've tried in order to get, um, I think its 3 keepers as repeats. As a scale, we are trying 40 varieties of tomatoes this year, only about 5 of which have done well for us in previous years, and only 3 of which we know are permanent to our list of varieties.
Edible-If I have a choice between edible and inedible of 2 things that will work well, edible wins 50-99% of the time. For my front flower garden, where I don't spend much time and is seen by everyone, edible is less important. Out back in the garden areas, edible is VERY important.
Yield-If it grows beautiful plants, but is supposed to fruit, it needs to fruit decently. If it can't ripen in time for my short season, or produces poorly, or the taste or texture is bad, out it goes. Though this is mainly for annuals like tomatoes and other vegetables. Looking at thrives in local gardens is usually a good indicator for perennials. Sometimes what does well is quite surprising.
In my head-I'm one of those people who are fairly visual internally, can keep track of lots of details in a loose manner, and can also do simple maths in my head so this works for me. I look at jotted notes and sketched notes and a multitude of sources over a period of hours to months and sort through ideas and let them percolate. Like
coffee, sometimes it take awhile to get the perfect brew.
Lists and diagrams:This works for my mom, who is very much not visual.
Sketchpads and drawing/printer paper-This is where I draw out comprehensive plans to see if they'll work, run them by my parents, and for implementation. Though I only do this for large areas. Small areas usually are fine with scrap paper sized sketches.
Good luck with your organizing and garden.