Try this:
Child1 c1Alias = null;
Child2 c2Alias = null;
var result = session.QueryOver<Parent>()
.InnerJoin(x => x.C1, () => c1Alias) // or use Left.JoinAlias
.InnerJoin(x => x.C2, () => c2Alias) // or use Left.JoinAlias
.Where(() => c1Alias.Id == 3)
.And(() => c2Alias.Id == 2)
.List();