Polysynthetic question

Hi all.

Well I completed my sandhi system for the daughter language of Ok. It
works pretty well but this has led me to another question.

How do native speakers of polysynthetic languages learn them?
Polysynthetic words are composed of roots that get strung together to
form "words" My question is do native speakers know the meaning of all
the roots or do they just learn the meaning of the "words"

The sandhi system (when it's applicable) of this 'daughter language'
disguises some of the roots so that it's hard to go back and decipher
what a word means later. because in my system when two consnants from
different roots fall next to each other, one gets dropped out or,
changes to a vowel. Whereas, when this happens with vowels, they combine
to form a different vowel.

I've been thinking that maybe I'd use a method like Irish where the
eclipsed consonant is still seen on the written word. but in this case
its just ugly and not very intuitive either. (as it regard
pronunciation)

So I'm thinking that I'm going to have to start a whole vocabulary of
poly-words as opposed to the vocabulary of 'just the roots' that I have
now. because my instinct tells me that people learn the 'words' rather
than all the roots.

Anybody?

-Duke