The Second and Third Clues

Begin it where warm waters halt 

And take it in the canyon down, 

Not far, but too far to walk. 

Put in below the home of Brown.

As I noted previously, many searchers break this stanza up into four clues:

1. Begin it where warm waters halt,

2. And take it in the canyon down,
3. Not far, but too far to walk.
4. Put in below the home of Brown.

In the second stanza, we have two sentences - and two clues.

How do I get from the above, to just two clues?  Like the first stanza - sentence structure.

Begin it where warm waters halt and take it in the canyon down, not far, but too far to walk.

That is a grammatically correct sentence.  

Waters is pluralized not because it is multiple waters, but so as not have to use the plurals of halt (halts) and take (takes) as that sounds awkward.  So instead you pluralize waters because they will do two things, the water will halt and take.

And they will halt and take "it" "in the canyon down, not far, but too far to walk."

Begin it where warm waters halt and take it in the canyon down, not far, but too far to walk.

THEN the next clue is Put in below the home of Brown.

Note: Brown is capitalized, indicated a proper noun.  Proper nouns have two distinct features: they name specific one-of-a-kind items, people or places, titles, etc. and they begin with capital letters, no matter where they occur within a sentence.  

Basically a proper noun "names" a common noun; where the restaurant in the shopping center is a common noun, The Taste of Thai is the proper noun.