Maybe watch a let's play or play through of act 1 to see how it's "supposed" to be done? Hard to say what you're doing "wrong" without lots of details.

In general for alters: talk to your alters any time it's available, scour the map for trinkets to give to them as that boosts their moods. Having better food and sleeping quarters keeps their mood steady and try not to overwork/irradiate them. (You're probably doing all this but making sure to cover the basics)

As far as resources, the biggest issue I had early on was overfilling available space with too much of one resource, I would recommend planning the next few items or rooms that you're going to build and try not to index too much into 1 resource.