How to know if your cat has herpes?

Chowder had some eye gunk (reddish brown) during the summer and when I asked about it I was told it was probably due to dust in the house or seasonal allergies.  It's still there! Could this be herpes virus?

It could be. Does he show the symptoms of a cold? Sneezing, runny nose, cough, etc. A lot of people call Herpes the Kitty Flu. It has some of the same symptoms. Mostly FHV is diagnosed by the symptoms. There are tests that will tell mostly for sure, but they are expensive.

It might be a good idea to start him on 250mg of L-lysine twice a day. Be sure to give him the doses 12 hours apart.

I haven't noticed any kind of a cough or runny nose, but he does sneeze sometimes.  He's also FIV+ so the lysine would probably help even if he doesn't have herpes.  I might try the Vetri-Lysine Plus chews.  He tends to do better with vitamin-like things when they're in treat form.  

Is their harm in giving lysine as a preventative or should you only give it during symptoms?

You'd get more 'bang for the buck' with the powder form. It's tasteless (though what is tasteless to humans is tasteful to cats).
And yes, given he is FIV+, L-lysine would probably help. You might discuss with your vet if he should be on a daily regime of L-lysine--cold or no cold. I volunteer for a cat sanctuary with around 100 cats (none are in cages unless they are sick or new), and all the cats (well and sick) get L-lysine in wet food one a day.

You would get even more 'bang for the buck' using the NOW brand of pure l-lysine powder from Amazon. The same price for four and a half times as much.