Roger is on it...never have, never will let the AI run my sub campaign. While the AI in general for this game is very good compared to any other computer game I've played, it doesn't "think".
I've done 2 PBEMs (disclosure, a@@ got kicked in the first one...) and "a few" tune up games as Allied vs AI. In my 2nd PBEM we're in pretty much the same spot (our game is in mid Apr 42).
Where to base...
You should have a number of AS ships, use them but be cautious about basing out of too many locations. Just because you have an AS available does not mean you need to open a new sub base. Check the manual, pg 287 has the listing of what's needed to rearm based on size of port in lieu of or in addition to AS ships. You'll also want to position ARs for repair where possible. I like;
Adak for covering East Coast of Japan, between Japan/Korea/Mongolia; in 42 just a few subs based here, all coming in as reinforcements. (as does the AS, through Panama @ Feb/March I think). You can eventually (usually by 43) build Adak up as a respectable port. Be wary of an IJ player who is aggressive in Aleutians. You may have to fight for it...
Central Japan, China Sea, Formosa, Einwok islands areas I cover from long range boats at Pearl. I deploy about 2/3 of Pearl's starting subs there, with limited reinforcements in '42. I don't bother to forward stage an AS to Midway in '42, leery of an early loss there and harassment. I will keep a couple of subs back for deploying harassing mines in IJ locations. (use the DMs to deploy defensive mines in conjunction with troop deployments to Midway/Baker/Canton, etc). Short range boats cover Wake/Midway/Johnson Island approaches as an early warning line.
The bulk of US subs start in Manilla, I send them out to Turk, Formosa, Philippines, South China, Vietnam, and Cebe Sea. The short range boats focus on defense of Philippines (between Phillp/Formosa around the Phillip beaches/approaches) remain based out of Manilla and will likely get one refuel there. The longer range boats I change the base to Darwin (Cebe), DEI (Saraj...something...the big port) (Viet/South China) or Sydney (Formosa/Turk & 1 or 2 East of the Philippines)during the initial turn(s). As the long range boats come into refuel the fight for the Philippines is usually about done and they get re-positioned to defend approaches to the DEI, New Guinea, Nomea, etc. The short range boats get shifted to Port Herden (sp? / NW Aussie) and Darwin to support DEI/Aussie defense.
US West Coast short range boats at the start of the game I deploy in a screen line beyond the range of my PBYs for an additional early warning barrier.
Dutch boats defend Eastern Malaya, N. Burma, and Cebe initially, rolling back to DEI as pressed by the IJ. The Dutch "O" boats deploy the Dutch sub mine arsenal at 2-3 area's I'm looking to make into strong points before going out on patrol duties (will take a few months ~ if you've not been leveraging sub mines...get to it!). As DEI falls, shift boats to Perth/Port Herden/Colombo. Be wary of overloading Darwin as your ability to get fuel into Darwin should the IJ press you there will get "difficult". (lesson learned the hard way...)
Reinforcements in '42:
Brit ~ all Indian ocean based, used almost exclusively in 42 to deploy mines (while they last)
US West Coast ~ short range boats to Pago Pago, long range to Adak then shifting to Pearl.
Panama ~ mix of Pago Pago and Sydney ~ depending on where the IJ seems to be pressing (Central Pacific or New Guinea/E Aussie area)
US East Coast ~ Port Herden/Perth or Colombo (depending on how well I'm doing in DEI) via Cape
Dutch ~ get a few boats that pop up, just add them into the DEI defense mix.
Manilla (usually falls by Mid March/Apr)
Saraj...(DEI, a few short range US Boats shifted from Manilla)
AS (AS comes from...) - Darwin (Manilla), Port Herden (Saraj or Manilla), Adak (US reinf.), Pago Pago (Pearl)
On a related topic...I've not seem much traffic on the "best IJ Merchant traffic lanes" to wait in. With PBEM I would assume your IJ counterpart will not let those fall to default routes (and your likely asking for a lot of merchant reefs if you only use computer generated as allied). In 42 I tend to play more "offensive-defense" using subs as early warning to what the IJ is up to, guarding key approaches to objectives, and watch a few choke points for tankers around Burma/Cebes with just enough subs around the home islands/China to keep him honest and using SCs, PBs, and DDs, etc in the rear areas. The AI is usually much, much more careless with guarding his merchants than a PBEM opponent. The AI also was more aggressive then my PBEM opponent in harassing West Coast ports and "cross" traffic between ports. Somewhere there was a good post for Allied players facing heavy US West Coast sub presence and shifting your shipping to only 1 or 2 heavily patrolled ports in '42.
If playing with realistic duds (the only way to play!)... don't get too frustrated in 42, your time will come. Even if you don't get massive sinkings, you'll be tying up ASW resources with your presence (at least that's what I keep telling myself )