Step 1. In the game click the EQ2 (StartButton), Select [Options], Select [Display]. 

Step 2. Go down the list and set each option of the display configurations to your custom preferences. 

Step 3. Click the [ACCEPT] Button. This is an important step!
Clicking the [ACCEPT] Button updates the eq2.recent.ini file.

Step 4. Press [ALT+ENTER] to go into Windowed Mode; Minimize the EQII Game Window. 

Step 5. Run the included utility program. Make sure your output folder is not the Video folder (you will need to do some notepad editing of the original files and the new files since the utility was not designed for my mod see step 12 below for more details)

Step 7. Select the button you want this profile to be saved to. 
Button #1 is the Raid Mode On. (custompreset1)
Button #2 is the Normal gameply Mode (custompreset2)
Button #3 is the Harvest Mode On (custompreset3)

Step 8. Select 'Kosmos Style' and Click 'GO'. 
This will Copy your Display Settings from the 'eq2_recent.ini' file
and create a new .XML file called 'eq2ui_custompreset*.xml'. 
The * will be the number associated with the button you have chosen. 

Step 9. Click [Exit] to close the Custom Preset Parser Window. 

Step 10. If you wish to create two additional profiles, return to the game window and continue from Step #1. 

Step 11. Once you have completed the creation of each of your profiles associated with the buttons exit the game. 

Step 12. Open up the newly created custompreset(s) file(s) in notepad. Should look something like this:

<?xml version="1.0" encoding="utf-8"?>
<Checkbox BackgroundColor="#FFFFFF" BackgroundOpacity="1.000" LocalTooltip="Raid Mode OFF" Location="145,16" Name="Custom2" OnSet="Parent.Custom1.checked=false Parent.Custom1.checked=false Parent.Custom3.checked=false Parent.Custom3.checked=false

[your settings should be here in between the above and below text at beginning and end of file, you want to copy all the settings files from the new preset but do not copy the text below or above the settings]

" ScrollExtent="14,15" Size="14,15" Style="CustomStyle" TextColor="#EBDEAA" Tooltip="Raid Mode OFF"></Checkbox>
<CheckboxStyle DisabledTextStyle="/Fonts.FontZapf15" Name="CustomStyle" NormalTextStyle="/Fonts.FontZapf15" RStyleActivated="CustomStyle.activated_rect" RStyleDefault="CustomStyle.default_rect" RStyleMouseOver="CustomStyle.default_mouseover_rect" RStyleMouseOverActivated="CustomStyle.activated_mouseover_rect"/>

Step 13. Now in notepad open the preset file in your customUI/video folder. Look for the same text (settings) and highlight or delete it then paste the copied text from the other file. That will keep your settings intact for the mod (button location and tooltips) but will have your desired settings associated with it now.

Step 14. Ok now click save, do not click save as (if you do click save as make sure you click ALL FILES, and not .txt). Next time you open EQ2 the preset files should be the way you want. 

Hope I didnt miss anything and that all makes sense, good luck with setting up your presets how you want them!