I made this little graph to show how certain types of quests will interact with the main story, which is obviously the black line in the middle.
The black line is the main storyline of the game. The end goal will be to build a large enough army and gain enough support and resources to defeat The Hog.
The red line is a very basic quest. It will start outside of the main story line, for example the player can just stumble into the quest giver in a random area. After completing the quest, the quest giver will contribute to the player's mission in some way, either joining their group, giving supplies, or even just "spreading" the word of the player mission which will unlock other quests and resources down the line.
The blue line is similar the red, however the quest line will continue at a later point in the game. The dot in the middle also shows that the quest completes outside of the main story, meaning the conflict is resolved and no immediate benefit is given back to the end goal. Then toward the end of the game extra resources will be given for completing the earlier quest.
The purple line shows a quest which begins outside the main story, and also doesn't giving anything towards it. Quest like these won't be very long or common, these will mostly silly and referential.
The green line is a modification on the blue. It begins from the main story, but doesn't have an origin for outside it. For example, this would be a side quest given by a character met in the main story, like the Ranger. It also resolves outside the main story and doesn't given any direct benefits, but will increase the relation with whatever character gave the quest. It also is connected to the purple line. Showing that completing the purple will have some effect when the player is completing the green.
Any combinations of these elements can be used to make quest lines, but I feel these best show how import side quest are the main story, and how they should be structured.