I love D&D Beyond, and have been using it a lot. I have also been using the encounter builder and combat tracker and it makes combats a breeze, especially since integration with Roll20, via Beyond20 app. However, I am getting set for a showdown between the players and a pseudo-villain the group has been chasing for a while. 

He is a higher level character, and has one of the previous PCs turned villain with him. I'd love to set up this encounter with the encounter builder, but there is no options to add a character from the character builder, without making them part of the party. Is there anyway around this? Also, if not, then I would like to suggest it to be an added feature for the encounter builder. Which I know is still in beta.

Are you trying to make the high lvl character a monster for the battle and would like to see them in the monster search or is having the character in the campaign causing balance issues with your encounters because he is in the party.

I was setting up an encounter with the party and 3 NPC characters (bad guys). I eneded up just adding them to the encounter once the encounter was running. Which works ok enough, but to determine CR for XP, I sort of reverse engineered it. I determined what CR of a creature would be a medium level challenge for each character by itself, and figured that they would be equivalent XP-wise for a creature of that CR.

I think the goal here is to be able to use the character builder to generate NPC's. You would not want to add them to the campaign/party, as this may give away too much information. These 'NPC' villain's/monsters should be selectable within the Encounter as opponents for the PC's.

I thought maybe I could at least Sub in a Homebrew monster, but Human is not even an option when creating a Monster. And there are definitely some humans out there that are truly monsters...

Quote from CobraCAO >>

I think the goal here is to be able to use the character builder to generate NPC's. You would not want to add them to the campaign/party, as this may give away too much information. These 'NPC' villain's/monsters should be selectable within the Encounter as opponents for the PC's.

I thought maybe I could at least Sub in a Homebrew monster, but Human is not even an option when creating a Monster. And there are definitely some humans out there that are truly monsters...

 "Human" might not be, but NPCs like Commoner, Archmage, druid, bandit and many more are.  

For example, see this list of NPC statblocks from the Basic Rules, all of which can be used as templates in Homebrew to create specialized version. 

This might help:

https://www.dndbeyond.com/forums/dungeons-dragons-discussion/homebrew-house-rules/132012-quick-customized-npcs

It’s all about making quick NPCs using PC builder tools and monster statblocks. It’s a quick easy way to generate unique NPCs in a minute or two, or for giving more in-depth thought to if necessary. 

How do i link an encounter to a campaign so the players can join

In the encounter builder you select the appropriate campaign instead of setting it to a number of generic PCs of appropriate levels. Click the dropdown and scroll all the way to be bottom and you’ll see your campaigns listed.

how do I add the PCs to the combat tracker?

Quote from Delazar >>

how do I add the PCs to the combat tracker?

 See the post just above yours. You tie the encounter to the campaign as Sposta explained. 

is there a way to add Conditions to the PCs/NPCs in the Combat Tracker?

Quote from Delazar >>

is there a way to add Conditions to the PCs/NPCs in the Combat Tracker?

 no. I think the team hoped to add it at some point, but no visible improvements have been made for some time.