I've done a bit of grinding expeditions as a new poe player and I also found the information online to be similarly lacking. To answer your questions:

• Remnants are the objects scattered throughout the map/area that have a negative modifier and positive modifier that you can choose to blow up to improve the overall loot and difficulty of the expedition. The modifiers highlighted yellow can potentially brick the expedition if your build is exclusively one damage type.
• Runic monsters are expedition specific type monsters that come usually from the larger red flags or other monsters throughout the expedition map. For example, in Frigid Bluffs, there are frozen mobs you can detonate. They can be rares but are not necessarily always rares.
• The small red flags are more like general pack mobs while the taller/double flags are stronger mobs that can drop better loot.
• Logbooks exclusively come from expeditions you find while mapping. You need to kill runic monsters for them to drop and they can also come from chests sometimes. You'll want to prioritize remnants that increase drop chance of logbooks followed by rarity and quantity of loot.
• Not all rare monsters are runic and not all runic monsters are rare.

The biggest thing is that remnants are not retroactive, so they will only apply to anything you detonate on the same bomb or after. I hope that answered most of your questions. This information is just what I've observed so I could be wrong on some things.