I have downloaded the most recent version of the Ultima 2 upgrade patch to deal with the horrid colors the base game has, along with the number-based bugs it's said to fix. I have followed the directions given to me, but now the game won't start at all, I have put below the instructions I was given any help will be greatly appreciated.
Installation:

1) Run the following program to patch the game, depending on your O/S:
* Windows: u2upw (Can be launched directly from explorer)
* DOS: u2up
2) Edit dosbox.conf (dosboxULTIMA2.conf for GOG) and change these values:
* cycles=10000 (or greater)
* cputype=auto
3) Run ULTIMA2.COM in DOSBOX to start the game.
* For GOG, edit dosboxULTIMA2_single.conf and change the line that
reads 'ultimaII.exe' to 'ULTIMA2.COM'.

Optional Steps:

*) Run the following program to change the default configuration:
* Windows: u2cfgw (Can be launched directly from explorer)
* DOS: u2cfg

Update: I managed to get the game to run, by moving files out of a subfolder and into the main ultima 2 folder instead, but now the game is running too fast to be useable, and it seems the patch didn't apply since it's still doing the old 4 base colors instead of the new ones I wanted. Any help on getting this working would be greatly appreciated.

I suspect that you have not installed the patch correctly. Please, state what you did in order to patch the game.

Ok, I downloaded the patch, then moved it into the ultima 2 folder in the games section of GOG Galaxy. I then unzipped it which made a folder, I then opened the u2upw file, then once I did that I opened the to Conf files in notepad, edited them as directed then saved them each in order. I then pulled all the files out of the folder they were in back to the Ultima 2 folder, which then allowed the game to work again. But still incorrectly. So I tried again, and this time it was different slightly as instead of opening the u2upw, I ran it as administrator, which says it did something but didn't seem to change anything. So if you have any advice I'd be glad to hear it.

Ok I followed the Instructions, and it seems to have worked, but I haven't been able to verify because I don't know how to actually run it on DOSBox, and I don't want to close it, in case that breaks it, it says run isn't a command you can use on DOSBox. What do I do instead? Also thanks for the help so far.
NVM: Figured it out, Thank you kindly for all the help.