Yes, it is OK to use "Ja nai ndakedo na " / "Ja nai ndakedo", but in this case, you had better complete a sentence just like " A Ja nai ndakedo na B" / "A Ja nai ndakedo B" (= even though ... not ..., B ), for example "(watashi wa) nihongo go ga mada jozu dewa nai keredomo... nihonjin to takusan hanashite mitai desu" , " shigoto ja nai ndakedo ... syumi de tudukete imasu." However, someone already said B in a certain context, you don't have to say more. The meaning varies to the context.
Pay attention! "...nai ndakedo" , "...ja nai ndakedo" are not really polite expressions although many people use them evey day. You'd better say, "...nai keredomo", "...de wa nai keredomo"