How to do Indirect Conditions

For example, consider the following conditions (from Wheelocks):

  1. Si id facit, prudens est.
    “If he is doing this, he is wise.” (present simple fact)

  2. Si id faceret, prudens esset.
    “If he were doing this [but is not], he would be wise.” (present contrary to fact)

How would you put these into indirect statements, e.g., “They thought that…”

I assume you leave the protasis (the “if” clause) alone and put the adoposis (result) in the accusative-infinitive form? But how do you distinguish between indicative and subjunctive if you must use the infinitive?

I assume the first would be:
Putabant si id facit, eum prudens esse.
“They thought that if he is doing this, he is wise.”

Then should the second be:
Putabant si id faceret, eum prudens esse.

Both “esse”? Even though one is fact and the other contrary to fact? Is the difference assumed from the protasis?

What about sequence of tenses?
Is the time of both the protasis and adoposis relative to that of the main clause?
Or is the time of one of the clauses relative to the time of the other?

In the above example:
Putabant si id facit, eum prudens esse.
“They thought that if he is doing this, he is wise.”
Are both clauses (present) taking place at the time they were thinking?

Or in
Putabant si id fecit, eum prudens futurus esse.
Is “fecit” before or at the same time as putabant (or would you need to use fecerat?) and
“futurus esse” in the future of putabant?

For this kind of thing Woodcock’s A New Latin Syntax is the best option. I’ve scanned his chart of conditionals in indirect discourse (oratio obliqua) - I don’t know how to include an image here in a Textkit post, but you can see the scanned chart here:
http://media.bestmoodle.net/Woodcock1.jpg

There are two more examples on the page following which I will just type here:
8. Future Logical
Si hoc dicet, errabit = No different from no. 7 in the chart.
Si hoc fecerit (fut pf.), poenas dabit.
Censeo, si hoc fecerit (pf. subj.), eum poenas daturum.
Censebam, si hoc fecisset, eum poenas daturum.

If you are interested in this advanced type of Latin syntax, Woodcock is definitely worth the price (about $25 at Amazon - http://tinyurl.com/6g4z5rl) - it is incredibly well-organized, thorough and very clear.