To assign some shortcuts to the applications you can use WPrefs program which is a part of Window Maker installation. In some versions of Window Maker the path to that program is /usr/bin/WPrefs so it’s enough to run it with simple command WPrefs. In the other versions the program lies deeper: /usr/lib/GNUstep/Applications/WPrefs.app/WPrefs. In such case it’s necessary to type full path to it.
To add a new item to Window Maker’s “Applications” menu you can use a ninth icon from the left in WPrefs window (it's named “Applications Menu Definition”). Using that option you can add new application to the menu and assign with it the preferred shortcut.
I prefer personally manual editing of the configuration files instead of use WPrefs. To add Gmrun to the menu you have to edit ~/GNUstep/Defaults/WMRootMenu file and insert in the appropriate place the following line:
(Gmrun, SHORTCUT, "Mod1+F2", EXEC, "gmrun"),
On the other hand I wonder whether using of Gmrun in Window Maker is reasonable. I have two arguments against it. First: Gmrun was designed to work with GNOME not with Window Maker. Second: as it seems the newest version of Gmrun is 0.9 and was released in 2003 so it’s very outdated.
I’m not sure what you mean when you write you’d move Dockapp to the other place.
In default configuration of Window Maker the top right edge of the screen is reserved for WMDock and WMClip. First serves to dock to it applications visible on the first workspace (these dockable applications occupy the top edge of the screen), and second serves to dock applications visible on all workspaces (these dockable applications occupy the right edge of the screen). I prefer personally keep WMDock and WMClip on the left upper edge of the screen so I drag them to that place using mouse.
In default configuration the bottom left edge of the screen occupy icons of running programs. To move them to another place it’s enough to run WPrefs, use a fourth icon from the left (it's named “Icon Preferences”), and select desirable position for those icons. I prefer personally the top right edge of the screen.
If you’d like to see my Window Maker desktop look here: This is my Slackware desktop...