you have a clone r4ds not the real one...
1.themes- go to the system folder and there should be a folder called theme(skin), and inside of it there are 12 folders, now replace the contents of it with ur skin. after that put ur flashcard in the ds and on the main menu press "select button" to change the skin.
2.no you cant have the same menu as the cyclo because r4ds doesnt support cyclo firmware.
3. what do you mean by linux? the real OS or the homebrew?