When you have chosen the WinAVR compiler for your project and the compiler options opened for example via Build - Set Compiler Options are not enough, you next better click on Build - Select Compiler.
In this dialog WinAVR - Application should be already preselected. Click on button Edit Configuration.
What you should first do is pressing button Make Configuration Local (Save in Project Directory) to avoid editing the WinAVR application configuration file in the configs subdirectory of UEStudio which is updated when updating UEStudio.
Alternatively when you will later need that configuration also for other projects, you can create in the configs subdirectory a new directory, for example My_WinAVR, and copy the standard WinAVR application file from subdirectory WinAVR Compiler into directory My_WinAVR.
Also possible is to just copy file Application in directory WinAVR Compiler into the same directory with another name like MyApplication.
Both alternatives make it possible for you to create your own configuration which you can use for all of your projects without be worried about overwriting the configuration on update of UEStudio.
As far as I know there is no better documentation for creating a compiler configuration file than what is found in help of UEStudio. So I write here some additional hints.
At top of the configuration file there are some comment lines which list the standard variables UEStudio offers for being used in the configuration. I think, I don't have to explain them more detailed.
What you see next are various sections [...] with various commands in the format name = value. What the sections are for and which commands are possible is explained in help of UEStudio. Open the help and select the tab Index where at top all the compiler sections are listed. Hint: Read the help pages for the sections in the order you can see the sections in the configuration file and not in alphabetical order as listed on help Index.
Take the time and read the help for the sections with using existing WinAVR or other configurations as reference. Most is quite easy to understand.
Of course you surely need also all the help files of WinAVR. Such a configuration is definitely not created in 2-3 hours because lots of text must be read, understand, used and the created configuration also tested. But the time spent is a good investment when the custom compiler configuration is finally working perfect for your needs and helps you in future working faster than with AVRStudio.
If you need detailed help for a specific configuration command or problem, please ask here in the forum or IDM support by email.
I must add something embarrassing for IDM and for Adobe. IDM has updated their Adobe RoboHelp installation a few months ago. RoboHelp is used for the CHM help. After update it happened that RoboHelp changed all the HTML files inside the CHM of UE/UES and reformatted the lines in the HTML file. RoboHelp ignored here completely the rule that browsers which display HTML files display a line termination inside a HTML file as space character when the first non whitespace string is not a HTML element or the line break is inside a HTML element. The result of this bad reformatting of the HTML code by RoboHelp is that in many, many help files now line terminations are present between two characters/strings which should not be separated by a line termination like $T. The result is that you see $ T instead of $T because of $\r\nT in the HTML source. IDM has not yet fixed all wrong line breaks causing a wrongly displayed space character on viewing the help page. I wrote this here because the help pages for the sections also contains such wrong spaces and therefore you must be careful on read and copy.
Best regards from Austria