From: The wilds of Caithness
Get your SUs into the command levels that directly control units - so most into the corps. Its a bit of a pity but the allocation routines don't work down the command layers (pity in that it means you can't hold key, rare, resources at say the army level).
The exception to this is construction engineers. The higher up the commmand chain the more flexible they are. So if you just accept they do their thing and it works out ok in the end, leave them at AFHQ/SHAEF or in the Army Grps. If you really want to repair structures and rails in a very narrow sector, place them in army or corps (they won't wander so far).
German stay behind ports can be a pain. First cut off sea supply and that is best done by placing a TF so that the TF ZoC covers the port sea hex but the TF is not actually adjacent to the port hex. If you can't spare a TF for this, then use naval air interdiction. Once its isolated it will start to degrade. Then attack, lots of combat engineers and heavy artillery. You may well fail a few times but sooner or later they will run down their supply/ammunition stocks. The AI really likes to build this type of defense and each can really slow you up.
You can mix nationalities with no penalty, either at command level (so a Polish corps can command US units) or by incl combat/support units in the same attack.
Yes you are right about the sep corps malus. If you mix commands the malus runs from 10% to 35% depending on how mixed. At worst, you use 2 divisions from different corps reporting to different armies that are, in turn, in different army groups. Depends on how critical/marginal the attack is, but against the AI I don't over-fuss about the corps penalty but keep your armies apart. Of course, there will be battles where even the 10% is critical (such as a port assault etc).