Yes, there's a free program called Ian Cooke. I'm kidding, but he does know a lot about planning gardens - he helped Tom and the YourGardenShow Italy team with some guidance on the Lisaland garden (it's like the YourGardenShow test kitchen!). I'll mention to Ian and Tom that you were asking about garden mapping programs and I'm sure they'll have a good suggestion!
We used the garden planner on Mother Earth News and it worked great (if I understand your needs correctly). Let me know if this scratches your itch. BTW, I think it's free for a bit and then you're asked to pay a modest sum.
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