You won't be able to "replace" the out of the box workflow  but after you deploy,
install, and activate your workflow Feature, it will show up in the dialog when
you try to associate workflows with a given list, just like the out of the box
workflow. It will also be included in the workflow gallery in the Site Settings
of the top-level site in the site collection.

Even i developed  similar kind of multilevel custom  work flow in publishing
portal using vs2008.one can remove the default approval  work flow from the
page.This can be done by removing the default xml and javascript tags related
to the approval workflo from the page .Use share point designer to do this.Lot
of material is provided in this regard,kindly search for one.If possible i will
try to pass you on some to you.

Else leave the default work flow intact and try to activate the work flow using
the workflow's option in the page.

By the way how did you manage to save the state of the applicaion . like in
default approval workflow  when an approver see's the updated document , he can
view the content which is updated in tags.