I go on a bit about the skill points for the Sacred Chambers, so here's a list of what gains and loses points, taken from Ultimortal's Kid Icarus FAQ on Gamefaqs:
-300 for taking damage, except for damage tiles like lava
-10 for firing an arrow
-500 for breaking a jar in the Treasure chamber
+300 for entering a Holy chamber
+100 for defeating an enemy that drops a small heart
+300 for defeating an enemy that drops a half heart
+500 for defeating an enemy that drops a big heart
+100 for collecting a small heart (if you have less than 998)
+300 for collecting a half heart (if you have less than 994)
+500 for collecting a big heart (if you have less than 989)
+100 for collecting a mallet
+1000 for collecting or buying back a Weapon
+100 for buying anything in a shop except a Glass or Weapon
+300 for entering the Score tally screen (redundant)
+8000 for killing a boss (redundant)
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