I’m not sure how to help you with your other concerns, but I can give you instructions to make your map work with Infection.
To set your map up for Infection, you need to place at least one Safe Haven on the map – even if Havens are disabled in the gametype you use. That is, add a Hill Marker with the INF_HAVEN gametype label. You also need to give the Humans some Red Team spawns, and give the Zombies some Blue Team spawns.
If any of that confused you, then keep reading.
Basically, you can create objectives on the map using a new feature in Reach called “gametype labels”. You take an object on your map, and give it a gametype label; when you play the map in Custom Games, that label determines what the object does. (So for example, if you apply the KOTH_HILL label to a Warthog, then that Warthog will be a Hill when you play KOTH.) This system is more complicated than the stuff used in Halo 3, but it has one key benefit: anything can be anything.
To create a Safe Haven, you must apply the INF_HAVEN label to something. Most people use labeled Hill Markers. You need at least one Haven on the map for the game to let you load Infection. If you actually want to use Safe Havens, then you’ll need at least two. (Reach only checks for one, but it’ll break mid-game if you have less than two.) No other labels are necessary.
Note that you cannot see a gametype’s labels unless you select it while in the Forge lobby. So to apply the INF_HAVEN label to something, you must select “INFECTION” instead of “BASIC EDITING”, and then start editing your map.