So I am in need of some decent strategy when it comes to defending the allied drive up from sicily and further.
Which air units to move, what loadouts, only focus on air superiority? Spread the planes across the entire southern end or just put them in places with flak?
It's really hard to offer specific advice because as the Axis a lot of your strategy is responsive, but here are some general things I've taken to doing. Can't say how they play out over the long term as my furthest game against an opponent is something like turn 24 now.
At the outset I like to re-organize the LW.
I pull my NFs and FBs under Luftflotte 3 to protect the Reich from the Allied murder campaign. Luftflotte 3 has a good commander, and not failing checks is always nice. As FB and NF air groups get chewed up I rotate them to Bavaria to recoup.
I put recon assets under Jagd I & II as well Flieger II. This way I can create discrete recon air directives for each of my recon air groups.
Flieger IX usually gets the patrol assets and maybe some recon. This is usually the only Air HQ that I leave auto naval patrol enabled.
Luftflotte 2 then becomes the LB force. I like to hide these puppies in the heart of Europe until they're needed to harass beaches and allied air fields. This Air HQ also starts with a good commander, so you can assign plenty of bombing directives. I transfer FBs between Luftflotte 3 and Luftflotte 2 as needed for escort purposes.
In the initial turns I tend to vacate useful Italian air bases of aircraft, switch them to OKL, and leave their TOE on AUTO so they switch nationality before the Italian surrender. Then I use the various Stab air groups to 'seed' supply to air bases I'm interested in maintaining in Italy and build up their TOE with manual settings.
You can then bring in air groups (change the air base HQ accordingly), launch a wave of attacks, and so long as you don't over use them and burn up their available miles you can transfer them back to safer air bases beyond the likely range of Allied retaliation.
I also like to send the Me 410s and Bf 110G-2s for retraining as bombers. Something about the interdiction engine favors multiple bomb loads (they can carry 8 and 10 bombs respectively), so they can give you some good interdiction value with decent legs. Nice to hit the WA on the turn you plan a counterattack to increase his retreat losses, as well as slowing pursuit of a withdrawal. Do it immediately and they should be available not long after the Allies try to get on the mainland of Italy.
Italian LW Command gets these retrained FBs as well as the FW 190s and recon/fighter assets as needs arise.