Polysynthesis and Clauses

I've been trying to grok polysynthetic langs for the last year or two.

From what I can tell (studying Mohawk and other Iroquoian langs, and
reading Mithun's _Languages of Native North America_), most polysynthetic
languages do not have the sort of hierarchical inter-word structure that
we are used to (relative clauses, complex and compound sentences, etc) -
in some languages, inter-word relationships are indicated by prosody;
in others, there are a limited number of prefixes that hint at a word's
place in the discourse.

Now, this is largely because the words *are* the clauses.  In fact, the
other day when I was trying to imagine how relative clauses *would* work
in a polysynthetic language, I realized that they may already be there;
a head noun could be incorporated into a clause/word, and the resulting
polysynthetic word would be both an argument of a predicate, and a clause.

But I don't know enough about it to know if this is indeed what's going
on - putting together one's own course of study in this area is difficult,
and I haven't taught myself as much as I wanted to learn.  When I read
interlinears of Mohawk text, I can't see how things relate; it still
looks like it's all just thrown in there as word salad.

I still want to make my own polysynthetic language.  I just have this
overwhelming urge to make the inter-word structure *explicit*.  I want
to inflect clause/words to show how they relate to each other.  Would I
be going entirely against the spirit of the thing?  Is explicit marking
of subordinate clauses antithetical to the entire nature of a polysynthetic
language?

Any advice would be appreciated.

Thanks,
Amanda