yeah, it takes a while to get things sorted, but by 6/42 you should be well-organized - all the low-endurance ships flee to Oz or India, the high-endurance ones go to CT. IMO you should use at least half your EC<>CT xAKs convoys w/ fuel for Cape Town, it's a bugger if CT dries up. early on (& later on as well) it's your on-map fuel convoys that need the most protection from raiders, your combat fleets need fuel to operate effectively, every time you lose a TK/AO you're losing a bit from your combat options. losing some of them is inevitable, losing a lot of them is avoidable!
early-war, check all your off-map bases & the on-map ports that receive their convoys. you need to build up these ports w/ engrs, & improve their un/load capacity w/ Navsupport - check these bases to turn replacements ON for LCUs that don't begin the game at full strength.
by mid-42 you'll start to get new AKs & TKs on the WC or at Balboa, check your ship reinforcement screen for new arrivals, send ASW ships to escort them from, say, Portland down to LA.
also, there's quite a few ships in the initial allied transport fleet that can be upgraded to APAs or AKAs. you need to find all these guys and send them to safety at Mare Island or Alameda, to await their upgrades. you're gonna need them all, to create effective AmphTFs.
Great info! A couple of follow ups:
In the west, I've been sending high-endurance TKs and AKs (including xAKs) to Capetown and the two off-maps locations north of India (Abadan and ???can't remember the name). I was then intending to send those units in CT to England to ship supplies and fuel, using CS: settings. When that stuff gets to CT, I'm sending it to Australia or Ceylon (most to Australia).
In the east, I wasn't sure how much needs to go through the Canal. Is it necessary to ship fuel/supplies from Eastern US through there? I thought that basically most of that should rail across the country, and that the time to get it where it's going is probably a wash.
I was aware that I needed to build up the ports/forts in various locations, and I've been doing that, as best I can (seems most units are [R], though). I'm not sure, though, what needs to be done to increase Naval support. I saw this was an issue, but wasn't sure what the remedy is.
I chose to basically evacuate Malaya and the Philippines of the units that could be moved. I probably should start using the option to reassign HQs to free up more units (or, is that not necessary?).
Oh, one other thing that's been bothering me--is there a penalty for mixing/matching your nationalities? I've got a TF with both Brit and US AKs, for example. Is that a problem?