Question about difficulty and progression

[Overdose]

I am in my first hours playing this game. The first few missions were easy, as I picked those with just 1 or 2 skull difficulty. Maybe 4-6 enemies across the level.
Now I am 4 hours in and on another 1-skull difficulty mission. There are 8-12 enemies per room and biocollapse chance is 80%, damage and health of the morphes boosted by 200%. Rooms are filled with those iron maiden quasimorphs, I wade through tons of loot, but have only a crappy tourist backpack (and this capsule just holds 2 units). Some tipps to have a better difficulty/progression/loot ratio in future?

Edit: when I go on a spionage mission for Faction A (Spionage; Force-concentration 500; 1-skull difficulty) against Faction B (Infiltration; Force-concentration 2500; 5-skull difficulty). For the Faction A run, which is the difficulty I have to look for? Is it a 1-skull rating for my mission or will I face the 5-skulls of Faction B?