I'm building some encounters where I want my party to have higher powered allies who will be fighting some of the higher powered enemies as a distraction while the party continues with their mission. Additionally, some of their enemies will be grievously injured at this point. Unfortunately, this makes it so that the encounter is rated as deadly even though many creatures are lower in health and working alongside them. Is there a way to mark this down in the encounter builder? I know it's currently in beta, but is there something that I am missing as a new DM?

The only way is to homebrew a creature and reduce its CR manually - the homebrewed copy could then be created with the lower hit points.

Or just accept that the encounter builder will mark it as deadly but YOU know it isn't.

Unfortunately, you can't input monster or sidekick allies. I really wish you could, though!

A shame, thanks for the help though!

TL;DR - There's a way to make it kinda work, but it's far from polished or what I would call "user friendly" in its current form.

So there is a way, but it's not the way that you're thinking, probably.  I dunno, maybe.... here goes.  Also, and this is a BIG caveat here - I'm not a professed expert on this subject, just a DM that's had to fumble through the process the trial-and-error method. I willingly concede that there are smarter folks out there and will welcome their tutelage at any moment.

So you can add additional characters to your encounter through the "manage characters" button in the encounter builder.  If you already have your players' characters linked to your campaign, the "add-on" character will show up as  a "Player Character - Level (insert number)" in the Combat Tracker. Drawback is that you would have to run the NPC manually with the generic dice roller and HP tracking tool. Unless you create the NPC as a character in you campaign. Then you can make the rolls from their Char Sheet as normal and it will show in the game log. Caution - looks, acts, and technically is a DMPC. You've been warned....

Second method... Use the "manual entry" button in the Combat Tracker to add the NPCs' stats (name, HP, AC, Speed, Initiative and Quantity). They will show up in the "Monster" half of the Combat Tracker and will still require the manual operation as described before.

Third method has already been suggested by Farling, they are spot on with their assessment IMHO.

Lastly, and this only applies to sidekicks, companions, familiars and the like.  In the "extras" tab of the character sheet, the player has the option to add one of several extras to their sheet that they can access during the game. I'm aware that this, in no way, helps with encounter balance issues or calculations, but that's the duct-tape version of making this work.  Good luck!

Thanks for more information on this. I think I'll most likely have to do a bunch of hard note taking in a Google Doc and have that up while I run my game. Thanks and best of luck to you and your games!

I don't have a solution for the second part of your question (about enemies who start out seriously wounded), but I can tell you how i handle the first.  In one of my campaigns, one of the characters has a wolf warrior sidekick.  There is also a wizard with a variant familiar (a "real' pseudodragon, using the Monster Manual rules).  I initially build out the encounter for the campaign, adding one additional character to the part of the requisite level.  (under manage characters).  I balance the encounter as desired.  Then I add in the homebrew stat blocks for the sidekick and the familiar.  The difficultly level will jump, but I ignore this.  I can then run the encounter with everyone involved in initiative order list. (I ignore the added character; with a 0 initiative, it drops to the bottom of the initiative list and is not in the way.