Wondrous things computers, and yes most design work nowadays is done on computer software. It would be fair to say that certifying authorities (internal and external) prefer to treat such computer output as "guilty until proven innocent", and a lot of testing work - structural and flight, is needed before the rest of us will trust our lives and careers to it.
The most well known design package used in the aircraft industry is "Catia", which is a huge mainframe based package that will allow huge design teams to work in parallel, with the computer ensuring that the electrical team isn't trying to put their cables through the same space as the systems team's hydraulics, and so-on. Boeings version will even allow maintenance experts to put on VR suits and helmets and try out all the maintenance tasks and ensure they can be done (as well as write the maintenance manuals before the aircraft's ever been built).
So far as wind tunnel testing is concerned, the same applies - whilst there's no substitute for testing, there are lots of predictive packages about. They are all bunched under the term of "CFD" or "Computational Fluid Dynamics". Generally a company will have bought-in a basic CFD package then will develop it to suit their own needs.
Detail design can be done on packages like Catia, but that's well out of reach of most companies, let-alone private individuals. The industry standard package for PC based design drawing is "Autocad", which is still quite expensive, but there's a much cheaper (and compatible) clone called "Turbocad" which you can buy for £10-£300 from Amazon (depending upon version).
Where you're talking about X-planes designer, that's really a conceptual design package, and is only making a stab-in-the-dark at the outline characteristics of a proposed design. Of course, it's great fun and ties up with a PC Flight Sim, but I wouldn't get carried away by thinking it's really designing an aeroplane. If you want to look at a reasonably serious piece of design software, I'd start
here . It'll do a lot of the donkey work for you.
But, frankly there's never going to be any subsitute for working through some serious textbooks and learning the basic theories and using them. I'd start by reading
Dan Raymer's simplified aircraft design for homebuilders which will show you the general idea. If that hasn't put you off (it's small but remarkably meaty), then download the
PFA Information Sheet and
BMAA Technical Information Leaflet that cover the practicalities and legalities of doing it in the UK. Join one or other association, and follow their recommended reading lists.
Well, that's my opinion anyway.
G