For someone so vocal about the short commings of each and every game manual out there you suck at conveying precise and detailed information yourself. Since you've negleted to indicate which mission those objectives refer to i'm going to go ahead and assume it's the mission Pyramida.
Capturing mechanics are most definitely covered in the manual. Here,
"CAPTURING ENERGY CORES
If you can cause a break in your enemy’s energy network, any of their Cores that become disconnected can be co-opted into your own power grid. Provided you have a working Energy Core close enough, any disconnected enemy Cores will be integrated into your system. Using your Perimeter Field, you can also force a break in an enemy’s network. If you have expanded your base close enough for your Perimeter Field to encompass one or more enemy Cores, any Cores (or buildings) inside your Perimeter will be cut off and linked into your network."
Basically you have to expand your energy network using energy cores (and energy transmitters) and connect your energy network to whatever it is you're trying to capture. If what you are trying to capture is not connected to the enemy's network, which is the case in Pyramida's scenario, then it's just a matter of expanding and getting there (and by getting there i mean expandind your network so that you can place an energy core next to the structure you're trying to capture). If what you're trying to capture is connected to the enemy's network then you'll have to cause a break in to disconnect the structure(s) in question from the enemy's network (or force your own Perimeter field on the enemy's network).
So, in regards to this specific mission, Pyramida, use energy transmitters (you can expand your network faster with them than with energy cores since they cover longer distances) to connect your power grid to 2 energy collectors (the big round things that increase the maximum ammount of energy that your network can have in storage). Notice though that transmitters unlike cores have no shields of their own so they're vulnerable break in points on your network. If required, say if if you need to place a transmitter someplace where you're constantly under attack from the scourge, put a core right next to the transmitter so that the core's shield can protect both core and transmitter (you have to manually turn on/off the shields of each core). Later on you'll have to mix this with units and laser/rocket towers to defend vulnerable spots, but on this mission core shields protecting a few of the transmitters and 20 or 30 soldiers to slowdown the scourge is more than enough.
Also, once you start moving up the map move your builmasters, you'll build faster if the buildmasters don't have to send building materials half way across the map. Building materials can be destroyed before reaching the building site, so that's another reason to keep your buildmasters as close as possible to the building site(s) while trying to keep them relatively safe at the same time. Another thing, try to evaluate what is it you need most for a particular scenario, fast terraforming (for building space or to quickly install your frame) or fast buiding (which is what you need in this scenario), and adjust your ratio of brigadiers/builmasters accordingly. And yet another thing, i'm under the impression that transmitters are only used to expand the network but they can't be used for capturing purposes, you'll need a core for that, although it's been a while since i've played Perimeter and i'm not entirely sure about this one.
The measure of sucess is if wether or not you can accomplish the mission objectives. Sometimes is charging a frame and leaving trough a portal, sometimes is powering an unpowered portal, sometimes it's destroying an enemy frame, sometimes capturing an enemy frame, whatever, read the mission objectives and that's what you have to do to move on.
The units are small but you can zoom in on the field (and units). In any case, squad management is best done from the squad palette. A double click on a squad portrait will center the view on the respective squad. The nanomorph palette provides you with all the necessary info on morphing options available and it even tells you what you're missing to acess other morphing options, so in terms of squad management that's basically all there is to it.
I'm not aware on any in depth guides. There's one
here with a few screenshots but i doubt that's what you're looking for.
Edit: Typos, lots of them.