The question was:
"I don't suppose there is an easy way to display and manipulate alternative side chains in O, or do I have to do lots of tedious editting and make new connectivity files etc???"
Thomas Schneider has done this already & has promised to make it available once he has a bit more time. For the time being, a useful hint (also from Thomas) for working with alternative conformations in O: read your molecule *twice* & use the second copy to fiddle with alternative conformations. After rebuilding, you'll have to do some file editing. This also assumes that no more than two conf. can be modelled, which is good practice according to George Sheldrick (his other recommendations in this respect: start the alt. conf. at CB; don't use alt. conf. for main-chain atoms; and use occupancies "p" and "(1-p)").