i personally would not use clockwork or rom manager

eek

lots of people may in fact use both,with no issue,but being active,here,on the d1,the inc,and now the thunderbolt forum,i see alot of scenarios like yours where the use of rom manager has led to disaster.
my advice would be to not use either. at the very least,id strongly reccomend getting the tracball optional recovery working,and becoming comfortable using it. then keep a couple nand backups from it,and a rom that you could flash in an emergency.
once youre comfortable with Amon_Ra,if you still feel the need to use rom manager or clockwork,go ahead. but at least youll have the tools and knowledge to fix a resulting bootloop or a semi-functioning rom with no rom manager and no market