Easiest method - use CKAN on PC and copy GameData folder over to steam deck:
Prerequisites:
- Have KSP and CKAN installed on a PC
- any Micro SD card (format the card to exFAT)
Step 1: install and apply all mods you want on CKAN and run KSP on PC
Step 2: plug in micro SD and copy the GameData folder from the PC installed KSP
Step 3: move the micro SD to the SteamDeck and open desktop mode
Step 4: copy and replace all contents of GameData folder to the steam deck ksp GameData. This is found in the Home directory under (“.local/share/Steam/steamapps/common/Kerbal Space Program”.)
you need to show hidden files by left clicking the finder window then “show hidden files”.