Standard Skills
Standard Skills in LOR refer to the normal skills that any character can go progress in. These are the normal skills that will often be found in.
Skills and Sub-skills
Sub-Skills are skills that are under a skill umbrella. Thus all bonuses that apply to skills apply to its sub-skill. For example a Lore bonus of +1 applies to all the lore subskills.
Advance Skills
Advance skills are skills that require special backstory, classes, or skill feats to gain proficiency in. If you have proficiency in them, you can increase proficiency in them in your class defined skill increase.