You can design in
permaculture lots of different ways. Designs can be done with complex computer programs with computer aided drafting (CAD) for beautiful realistic examples of how to shape the property.
Designs can also be done with pen/pencil/crayon/whatever else on paper/napkins/whatever other else for just as beautiful or even just very sketchy/scratchy/quick outlines of simplified things to do to shape the property.
Designs can even be done in your head and never be written down, drawn, or computerized.
In the end, the important thing is that a design was well thought out through zone planning, sector analysis, and observation of the existing property.
Remember that any design
should be considered a suggestion subject to change. You can picture a pretty
pond in your head all you want, but if you start digging and find out that there's not
enough clay there (or anywhere else on the property) then maybe some other tactic is needed for that slow it, spread it, sink it end result.
Having said all that, there's nothing WRONG with using a computer to do your designs, either. If you have the technology, and the talent/skill to take advantage of it, there's no reason it shouldn't be an option.