invading an atoll is a different animal from an invading an ordinary base - the atoll has v. small stacking limit, & invading troops will auto-shock attack immediately in the turn it unloads. here are some tips that are good for all invasions, the ones marked -*- apply only to atoll assaults.
- during load-out, use as many amph-type ships as possible (APA/AKA/LST) for your combat units, to maximize the amount of supply they load. if you need add'l supply, create a separate AmphTF, load supply, & merge it w/ your main AmphTF on the way to the target. if any of the supply-column ships load fuel, keep them in a separate AmphTF (or merge them w/ a 3rd AmphTF that carries your post-victory garrison forces). Fuel-carrying transports burn really well if they get tagged by coastal gunfire. don't trust the transport load screen, it doesn't adjust for the 20% load-reduction that simulates combat-loading for the AmphTF. there's nothing more annoying than being well on your way, then discovering that many of your LCUs have left support elements behind.
- AmphTF size limit is 100 ships. Include combatants for gunfire support - anything w/ 5" guns or better, they magnet coastal gunfire & shoot back to suppress it. They'll use all their gun ammo, so be prepared to swap them w/ fresh combatants from your 2nd-wave AmphTF. They'll still have AA & ASW ammo.
- if available, use a ForceHQ - give it your manliest leader & load it to a separate AmphTF consisting of 1 AGC, merge it to your main AmphTF while en route. this combo improves unloading, & the leader will influence land combat while still embarked.
- set the AmphTF(s) destination to 'remain on station' one hex down-threat from the target hex. this hex is your Amph Ops Area (AOA) for staging your attack. when the AmphTF gets there, set it to remain on station, full speed and sail to the target hex. this will maximize the time your ships have available to unload in the subsequent night turn.
- manage your TFs carefully for day 2 - leave any hopeless cripples in the unloading TF as gunfire magnets, swap out damaged/empty transports & ammo-expended combatants w/ ships from the 2nd wave in the AOA. your ForceHQ/AGC combo won't unload until all other ships in the TF are empty, usually you can arrange things so that it never actually has to unload.
-*- assuming your atoll invasion didn't get waxed on turn 1, continue the assault by unloading large amounts of supply, most of which will disappear b/c of overstacking. as soon as you've wiped out the defenders, start re-loading the LCUs (use load troops only), else they'll start to disrupt due to overstacking. an atoll can hold 6,000 troops, you can exceed this by about 10% w/o taking a large hit, but more than that will damage your units.
- when withdrawing your ships, especially damaged ones, continue to sail in convoy. create an EscortTF for cripples, set it to cruise speed to minimize add'l damage as they head home.
- Sardaukar gave good tips above, i'd add a minesweeperTF to the list. it must go in first! it'll likely get creamed by CD guns, but that's the price of doing business.