I've been using DOSBox for a while, but I'm still a little confused as to how certain aspects work, so this is to hopefully clear up some of that.

While looking for a way to disable vertical mouse movement in DOSBox, I came across David Walters' custom build. Although I knew that using novert was an option, I think David's works better because the specific feature he includes - mouse vertical scaling - allows me to disable vertical mouse (by setting it to 0), as well as using its designed purpose to fix differing horizontal and vertical sensitivity issues in other games. So it's a more "complete" solution for me.

Anyway, one of the games I have installed is Blake Stone: Aliens of Gold. So can I simply Overwrite the dosbox.exe, SDL.dll, SDL_net.dll, and dosbox.conf files in the GOG folder with the files from David's build, and everything should work fine, without conflicts?

One specific problem is that GOG uses two separate .conf files. For Blake Stone, one is labeled dosboxBlakeAOG and the other (which contains the autoexec commands) is dosboxBlakeAOG_single. So here's what I'm planning on doing:

1) Edit David's dosbox.conf file to delete the [ipx] and [autoexec] sections at the end
2) Rename David's dosbox.conf to dosboxBlakeAOG.conf and overwrite the GOG version with it.
3) Leave the GOG dosboxBlakeAOG_single.conf as it is, without changes.

I have tried all of this already, and it seems to be working fine. I just want to see if there's any potential issues that could come up.

As long as nothing in GoG's config files overwrites anything important in your config file, you should be fine.

Sometimes newer versions of DosBox will break compatibility with some games. It's rare, and from what I could tell gets fixed.

But beyond that, I don't see why you shouldn't. I mean DosBox is free software, and if you break the game all you have to do is re-install it again...

Ah that clears some things up a bit. So, here are the lines currently in my dosboxBlakeAOG_single.conf under [autoexec]:

@ECHO OFF
mount C ".."
c:
cls
BS_AOG.EXE
exit

I think I know what all of this does, except for 'cls' - Is that to clear the screen or something?

But, I understand your instructions and it makes good sense. I'll see if I can set it up this way.

Correct, cls just clears the screen.

One thing I forgot was that in DOSBox' global DOSBox.conf file already exists an [autoexec] section, which usually mounts one of your folders as C:\
That's the folder where you should have copied your game.
Now don't use the mount command from dosboxBlakeAOG_single.conf in your start.bat file.

In this game, you only need to start BS_AOG.EXE, everything else is not needed.
@ECHO OFF means, that the following commands don't show up in the window (no need to hide them imo)
mount C ".." is NOT needed, because when you start DOSBox there's already a folder mounted and functioning as C:\
c: is not needed, because it changes your location to C:\, but you're already there when you start DOSBox
cls not needed, just clears all previous text from the DOSBox window
BS_AOG.EXE the only important command, as this starts the game
exit is optional, it closes the DOSBox window after you exit the game (you can close it manually as well)

In this simple case, you don't even need a batch file, but could type in the commands yourself.
- Start DOSBox and you should find yourself at C:\
- Now change your directory to the game's folder by typing cd and the name of the folder
e.g. cd BS_AOG
This would bring you to C:\BS_AOG
If you don't know the folder name, use "dir" to list all folders of your current location (in this case C:\) and type it exactly like written there.
Once you're in the game's folder, just enter the name of the executable file to start it (in this case BS_AOG.EXE)
Just like in good old DOS times ;-)