An encounter is any meeting between the characters and their enemies (or creatures who may become their enemies). Often these will result in the two sides fighting, but they can be encounters based on social skills.
What's the Point?
The first step of a Game Leader is to decide what they wish the encounter to achieve. How does this encounter fit into the character's narrative?
The point of the encounter could be as simple as 'to have a fight' but there is a lot more scope than that. It might introduce the characters to a new type of monster, allow the players to find a map or be the final showdown between the characters and their arch-nemesis.
Understanding what the encounter should achieve makes planning it much easier.
When and Where
The setting for the encounter will make a large difference to the strength of the creatures needed for a challenging fight. If the characters will be in a heavily fortified position the monsters will need to have more CP to cope with the cover and other advantages the characters will receive. If the situation is reversed, the CP per creature needs to be lower.
Creatures designed for particular situations or environments generally need less CP than more general creatures. For example, a giant spider who can climb the walls of its cavern to outflank the party is more of a threat than a goblin with the same CP in the same cavern.
The scope of the encounter area should be as large as possible to give characters and creatures room to manoeuvre or run away as needed. The more space available the more options both sides have, giving characters a chance to use a greater variety of cards. Fights in narrow corridors do have their place but they tend to limit players to a narrow range of cards and tactics.
One, A Few or Many
Perhaps the most difficult aspect of planning an encounter is how many creatures to put into it. Because of the dangers the creatures (and characters) face in a two-on-one situation, too many monsters will kill the party but too few will not be a challenge.
In the 6d6 RPG there is no recipe that can be followed to produce the perfectly mathematically balanced encounter. Too many factors are involved, including the skill (or lack of it) the players exercise in the combat. Being a Game Leader is an art not a science and it can only be learnt through practice.
Designing the encounter with multiple waves of enemies is a good way to balance the fight. If the first wave is quickly dealt with, the second and third waves can combine. But if the first wave is giving the party a serious challenge the other waves can simply be forgotten.
With a single monster versus a group of characters it is very hard to create a challenging fight. The party can simply overwhelm the creature with weight of numbers and concentrated fire power. 'Boss' monsters or similar solitary creatures need to have the terrain and the circumstances in their favour to minimise the disadvantages of being outnumbered.