Hi @SYakubson ,
There's different ways to develop custom application running on the board.
Simplest way is cross-compiling your application on host PC making use of the Yocto SDK then transfer the binary to the board for execution. In order to install the SDK (including toolchain, libraries, ...) for cross-compiling, you will need to bitbake the image from scratch and then populate the SDK following instruction in the i.MX_Yocto_Project_User's_Guide.pdf found in every BSP's release documentation. There's good wiki for building and installing the Yocto SDK here : https://variwiki.com/index.php?title=Yocto_Toolchain_installation&release=RELEASE_SUMO_V1.6_DART-MX8...
More sophisticated way would be creating a Yocto based package (recipes, layers, ...) for your application then integrate it into the bitbaking system of Yocto/OpenEmbededed.
Or, you could find another way to compile natively your application on board with other flavors of distribution running on your iMX8M Mini such as Ubuntu/Debian (I don't know if it is possible to do that within the official Yocto Zeus distribution provided by NXP since I've never tried) if you are not hurry and your system have enough memory as well as you don't mind killing your SD card or eMMC after a while.
Regards,
K.