I'm using this Program SIMCON since the first issue some years ago.
Yes, the description Manual .pdf file is a bit confusing.
The program itself, without any doubt, is one of the best available.
I'm using the same program you are using. Never seen any bug.
The program is quite advanced what programming is concerned but not easy to use for anyone.
All data is calculated with real world mathe by Edd Williams.
As far as the virtual runway and virtual "Waypoint" is concerned you get it:
On Top (left) there are 6 Buttons.
ALT, AP, Hdg are connecting to the Autopilot
R, W, V are automatic Fly-To buttons.
R = the runway approach
W = you fly to the virtual Wpt at 20nm rwy-distance, alligned with the RWY. (you never miss the Rwy Hdg)
V = start the virtual Runway at any world position. Grd, Air, Sea. With the virtual Rwy you can use both the virtual (W)pt Heading and ®wy-Approach automatic.
Land on the Sea. Select 'V'. Start and Take off and return to the virtual Rwy created. Fly to (W) then turn to ®-unway approach.
Fly over a Rwy and click 'V'. fly around and you are Landing on that Rwy.
The panel below is also a Fly-To Panel. ADF, VOR, FIX wpt.
The Fly-To button is starting the automatic Fly-to > the one selected, Adv, Vor, Fix.
On Top at the right side with the A,V,N,I buttons you choose the Apt, Rwy, Vor, Adf, Fix.
The 'J' button is connecting to the Joystick and the Joystick Editor.
The 'Pilot' button is opening the Pilot Panel that is executing 'Mouseclick files' you create and also including the Simcon Help-Interface.
Concerning the GUI. The resolution is set properly.
There is no problem here, with Win 7 you should use "Windows Classic", with Win 8+, Win 10 you have the best appearance.
When opening the program a "System Tray" Menu is available. (status bar > right side)
Select "update" and you connect to the official Web-Page.
Now the SIMCON version 1.5.6 is available.
This update is including very important updates like:
Many Tooltips. Just Mouse Hover over all buttons, labels ecc.
On Radar > Descentometer (V/S dist) and the universal Glide-Path automatic Landing System.
Simcon is also connecting to a real world Flight Center.
There is no overlay of Panels.
Move a Panel like Radar, Pilot to any place. Close Simcon and reopen. All panels are placed where you left them.
There is no hidden area.
Info: the small "T" buttons are selecting/deselecting "stay on Top".
Get the latest Simcon update v 1.5.6.
You must write to the Author as mentioned under "Customer News: (x Simcon user)
Send a e-mail and indicate your SimMarket 'order number'.
You get immediate answer and assistance.
The program Manual is not the best, the assistance yes.
By the way: The smaller ATIasHold program, v 1.6, is now the most advanced of all programs.
When you ask for the update you will also get a Download Link x this programs that is using 2 Radars.
Hope this was helpful.