There are few messages regarding this stuff from Elf that can be found on somewhere between pages 10 and 14 here. He also responded again to a similar query, and that response should be on page 1 or 2 by now.
I believe the CRC radar and the SOC radar, as well as the objects tagged simply "Radar" in some of the SAM sites are there only as GCI "anchors" - if you don't use GCI linking, those objects don't do anything in the sim. For example, there are two radars on the SA-10C plugin, but only one actually appears in the TEWS and the HARM screen, whereas the other one (which shows up as "Command APC" if you destroy it) is the one that is used for GCI linking.
A site can only have one parent. As Elf pointed out, you want to make parent sites the SOC and CRCs, as they are silent and don't show up as emitters. If you make a SAM or EWR a parent, that branch of the network is easily degraded by HARMing that emitter and destroying the link between all those children. Since the CRC and SOC don't broadcast, only good intel would allow you to target those sites, so they make great parents.
From Elf's posts, I don't think the comm relay centers have any effect on GCI. I'm assuming the implied logic is that the GCI links are land lines.
Regarding taking down a branch, I think it would depend on what the parent plugin was, and which component actually was destroyed. For example, if you make an SA-10C site a parent (bad idea but good for example), if you HARMed that site only the fire control radar would be destroyed. The Command APC/GCI anchor would not be destroyed, so those children would still be linked. (If you dropped a Mk84 and wiped out the command apc, then the children would be offline.)
However, if the parent is an EWR, that radar is also the GCI anchor, so destroying the radar destroys the link for those children. Again, this points to the CRCs and SOCs as ideal parents.
I had written previously that I set up GCI by laying out EWR and SAM sites, then defining logical zones/sectors/regions, and then placing a CRC in each z/s/r. That CRC becomes the parent to all SAMs/AAA/EWRs in that zone. Repeat for each zone. I then add a SOC to the map, and link all the CRCs to that SOC. None of the hubs/parents are emitters, each zone has multiple shooters and sensors, and the entire AAW picture is fused at one master location, the SOC.
Per Elf's posts, this would seem to give the most efficient results for his coding of GCI.
RE: Campaign template issues, search through some of the previous pages here, and check out JayP's site on campaign building. The limits are known, and very high.
Personally, I wouldn't use a prebuilt air defense template, b/c you won't want that many resources gone for many parts of the map that are inconsequential to the campaign...likewise many of the plugins I would place for the campaign I would want to have included in the air defense plan - you won't know what areas to really saturate with AAW assets unless you know the value of the plugins that will be in that area in the campaign. Just my opinion!