As Tcby said it is probably best to ask these sort of questions in the other forum where more people will look at them. But I'll try to answer what I can...
One of the great things about DW though (unlike most other games) is there are many ways to approach promlems and no one solutions will always be the best one each time.
Yes, the playing through does show a high level of attention to resources and highlights the impact of stoppages due to resource shortages. It seems the quickest way to find out what is short is the alerts and cycling through colonies, and the quickest response is to ask smugglers to fill the gap.
Getting it more directly seems considerably more involved. The UI offers a number of ways to get slices of information about resource demand and locations, but if there is an integrated view showing the options I must be missing it. The empire sidebar can make it easy to see listed items identified on the map when mousing over. There isn't a resources bar there.
I can get information on a list of known available resource locations in the expansion planner and the general location on the minimap with it. I believe this excludes locations occupied by others. I can get locations highlighted more usefully on the "Galaxy" Map by selecting the chosen resource in the dropdown, but need to go to the expansion planner or click through to the location for more details. Or we can click on entire systems to get a complete resource overview and evaluation of the neighborhood and what may be safe. Stumbling through these tools I manage to miss rich targets that are enemy controlled worlds.
What is the best way to handle this?
Larry is great at sorting through the resources quickly so I'd recommend looking at his Part 1 videos. He uses the expansion planner mainly for this.
My method is to just focus on the 'difficult' resources that are needed for most construction: polymer, chromium and carbon fibre. I also like to directly control 2 or 3 steel sources in or close to my home world. I use the galaxy map for this.
Also, when you are building things you will get a list of required resources that are needed if you select the construction object. Any that it doesn't have enough of show in orange.
Pirate smuggling missions are a great source while they are in control of space. In our LP we have now turned a corner where the pirates are weaker than the empires so they will have less infrastructure to meet our demands. Early on the smuggling missions were the best source for us but now we need to start securing our own or get friends we can trade with. This was one of the reasons I shared the Zentabia Fluid in my last turn. :)
Assuming players use the double-handful of Ctrl keys for key fleets and ships, what do good players use as a checklist of things to return to later on? Other than noting it mentally or by hand or by renaming things in the game, are there game elements or mods that can help pin things on the map or tag them for later attention?
It would be great to have a notes ability within the game. What I do for recording is write notes in a text file then try to address each item. If I am just playing for fun I occasionally just scroll through special locations; the galaxy map at the special resources; potential colonies; and then just figure out what I'm going to target next.
In our game (in my opinion) all we need to really focus on are: Protecting the home world system; securing and eventually building a star port on Zentabia; securing the captured independent planets with the high populations (so we get tax income); keeping an eye on the Korrabian Spice and the Loros Fruit planets; capturing the other Keskadon planet from the humans; and capturing the Carrida Weapons facility from the humans. Most of the other planets don't add much to our income yet and in fact drain our income for the short-term until they develop.
To put this in perspective, in our current game I think we control 11 planets yet I think our home world generates over 95% of our income.
P.S. I like a medium to large map with a lot of stars. Is there a search function by name for known systems or astronomical objects?
A search/filter function would be very useful but it doesn't exist in the game
On the easier side, the Human war shows dramatically how important it is to know your enemy and tailor forces to fight them. I usually have preferred longer-range weapons so it hasn't been as forcefully presented. So boarding pods to capture ships are extra useful even if not a pirate.
I personally don't rely on capturing ships and generally prefer long range weapons. But in this game they weren't available to us so we had to re-design around what we had also keeping in mind we were a long way behind in research. Once again, the game presents a unique problem I personally have never had to consider before. :)
If you raise troops from conquered populations, are they liable to revolt, and more so if left on a planet of their species rather than sent to police other species?
I don't know the answer to that. I suspect not, but sometimes it seems your troops disappear when a rebellion starts. I'm not sure about the morale of those troops. Would be interested in the answer though. :)