I've noticed that some games like QFG games need some tinkering to get working well, eg. Quest for Glory games often need to have the speed cycles increased in order not to have too long loading times, however when the games are run through GOG you cannot do it as the buttons that change the speed cycle don't work (unlike when the games are run through normal Dosbox). And it's also not possible to access the setup so I can select different audio types, at least the setup is missing from my folders and those that aren't can't be run because I have a 64-bit Windows.

So my question is, is there any way how to access setup of every GOG game that has it (or should have it, I'm pretty sure if I were to use my CDs QFG1 and 3 would still have a separate setup.exe and not just an install.exe).

Secondly, is there any way how to configure Dosbox when running a GOG game?

Thirdly, what is the GOGDOSBOXCONFIG.exe (is it a configuration menu like I guess) and how do you run it? When I click on it, it says it can be only run from the start menu however it's missing from the start menu, so there's no way how to run it.

I'm guessing yer right about what it is - and it appeared in my start menu last night for some reason.
Beyond that, I have no idea I'm afraid.

Does it work? Try clicking on it and see what happens. :) It's not in mine, it's only in the GOG folder on C:/QFG/DOSBOX.

I'm not sure about Quest for Glory since I never played that game, but usually they should include the game's set-up files to configure the in-game settings. There should be some shortcuts in the root of your game's installation folder with "Launch Settings" or something similar along with a bunch of *conf files with file names such as "dosboxT2K_setting.conf" for Tyrian 2000 that handles running the game's setup files. If not, you can always create a DOSBox shortcut, move it to the root of your installation where it has those *conf files, then add [-conf "dosbox<gametitle>.conf" -conf "dosbox<gametitle_setup>.conf"] to the target properties (minus the brackets). As for GOGDOSConfig.exe, I think you can only run it with a shortcut or command line perimeters. If you take a look at the shortcut properties of something like "Launch Graphic Mode Setup" for Tyrian 2000 that has the orange/yellow GOG.com icon, there will be something next to the command line like "GOGTYRIAN2000" at the end of it to bring up the GOG config menu. It's possible to create a *bat file to run those commands as well.

Yeah, I do have the conf files but I was hoping it'd be possible to run the game's normal setup so I won't have to play around with those command lines, esp. since QFG VGA's conf file has for some reason no break lines, so it's all jumbled together and is very hard to get through. And yep, I just had a look at the Graphic mode of my games and you're right, the GOGDOSConfig.exe is listed in all of them. Thanks for the info! :)You're right after all, it worked! So I can speed them up, but so far it helps only so-so, during the game it's fine but the character selection is still a bit laggy. Although it might've been that way in the original too, but for some reason I do feel like it went usually smoothly and you had to click only on the profession once.

The problem is the old setup files are missing from QFG, so I can't use them and have to use the config fiels as suggested by AmethystViper and GOGDOSConfig.exe does show ups only in the game's folder but it doesn't work there, like I said, it just tells you to run it from Start Menu where it doesn't show up (neither through the search function nor the Start Menu's folders).

The line break thing is a dumb side effect of GOG's formatting in the .conf files. Try notepad++ (it's free), which makes editing those files much more convenient.

GOGDOSconfig.exe is just the "Launch Graphic Mode Setup" or "Dosbox Configurator" option, of which you should be able to find a shortcut in each game's subdirectory. It is, as has been mentioned, extremely limited (you can only tinker with the Graphic Mode; Full Screen; Aspect Ratio; Double Buffering; Scaling Engine; Window Resolution and Mouse Sensitivity).
For something like the DOSbox cycles, you need to access the .conf file.

It should be noted that you can use Quest for Glory's original setup programs (called either INST.EXE or INSTALL.EXE, just look in the directory) to change audio options and such. To do so, you just need Dosbox to launch with those instead of the game's executable (called either SCIV.EXE, SIERRA.EXE or SCIDHUV.EXE).
You can do that by opening the other .conf file ("dosboxQG1VGA_single.conf"), which contains the DOS commands that will start the game. There, change the line containing the game's .exe to that of the setup file (for example, SCIDHUV.EXE to INSTALL.EXE). Save it and launch the game's regular shortcut. Remember to change the command back afterwards; and always make a backup of the .conf file before changing anything.

It's the file dosboxTR.conf to change the resolution of the game manually, first lines after the commented lines with a #:

fullscreen=true
fulldouble=true
fullresolution=1024x768
windowresolution=640x480
output=direct3d

A tips it's to replace the missed up file with the one in Dosbox folder (copy dosbox.conf --> parent folder --> paste and replace dosboxTR.conf) edit it in the end.