1) If i had 1 Company Command Squad with Lord Creed (or whoever) would that count as 2 HQ choices or only 1
4) It keeps on saying in the codex that "replace sergeant with so and so" When i replace the seargent does the new sergeant count as a HQ
The options you're referring to are what are called "Upgrade Characters." They do not take up any additional slots or change the unit's Force Organization in any way, they simply replace the appropriate model. For example, you may replace the Company Commander in a Company Command Squad with either Lord Creed or Colonel Straken. The squad is still a single HQ choice and is still a Company Command Squad, it just happens to be led by/contain that character. The same is true of the other upgrade characters - Al'Rahem's squad is still a Platoon Command Squad (Troops), Bastonne's squad is still a Veteran Squad (Troops), Mogul Kamir's squad is still a Rough Rider Squad (Fast Attack), etc.
2) In a platoon if a command squad is let's say 9 inches away from the nearest infantry squad can the infantry squad still shoot and what happens if the command squad dies, Is the entire platoon then useless?
A Platoon Command Squad is simply a squad of four Guardsmen and one Platoon Commander. They and their partnered infantry squads act completely independently. You can deploy each part of an infantry platoon in entirely different places, and each unit is fully capable of acting on its own. The only reason they're usually clustered together is take advantage of the PCS's Orders, which have a relatively short range.
3) What is a Commissar, is it a HQ or what?
There are two types of Commissars. Lord Commissars are Independent Characters and are an HQ choice for Imperial Guard. Regular Commissars are upgrades that can be bought as additions to certain units. Regular Commissars are much like upgrade characters except they don't replace an existing model, they are simply added to the squad.