Preparing development environment (for maintainers)

Install Inno Setup 5 non-unicode: http://www.jrsoftware.org/isdl.php (isetup-5.x.x-unicode.exe).
Install kSignCMD: http://codesigning.ksoftware.net/ (click "Download kSign" and then "FREE DOWNLOAD" or "Click Here to Download kSign", which will likely be a link to http://cdn1.ksoftware.net/ksign_installer.exe)
Install the docker-code-signing.pfx certificate somewhere (the instructions below assume Z:\sven\src\docker\windows-installer\docker-code-signing.pfx); you will need the password (d_get_from_core below).
Open Toolbox.iss in the Inno Setup Compiler. It has a few constants at the top that are important to make note of (especially MyAppVersion and the path variables dockerCli, dockerMachineCli, kitematicSetup, b2dIso, msysGit, virtualBoxMsi, and virtualBoxCommon).
Launch Inno Setup Compiler by opening Toolbox.iss and add code signing by applying the following steps:

Click "Tools" --> "Configure Sign Tools" > "Add"
"Name of the Sign Tool:" ksign
"Command of the Sign Tool:" "C:\Program Files (x86)\kSign\kSignCMD.exe" /f Z:\sven\src\docker\windows-installer\docker-code-signing.pfx /p d_get_from_core $p

Releasing a new version

Update the versions of the dependencies in bundle.sh.

Update #define MyAppVersion line in Toolbox.iss.

Open a git bash window in this directory and run script:

./bundle.sh

This should be downloading dependencies with their correct versions to bundle\ folder where the Inno Setup Compiler can pick up from.

After configuring, open Toolbox.iss with Inno Setup Compiler and hit 'Build'. The results will be in the Output folder.

This can be done through commandline as welll. Launch a cmd.exe shell from this directory and run:

"c:\Program Files (x86)\Inno Setup 5\ISCC.exe" Toolbox.iss