I would not break down the bunks unless the space is large kids need a space to play in their bedroom IMO. As for the colors I always keep walls neutral and use the color of theyear for bedding decals anything easily changed . You should be able to upload a photo from your phone.

I would do a tone of their colors. For example, a bit of a burnt yellow. This one is from Target and is more muted than the first photo and it's really good:

^^closer to the actual color IRL

I would then incorporate a lot of other colors and patterns to avoid the "Mcdonald's" vibe like a blue rug with a more fun pattern to incorporate:

Cheetah table lamp

A picture of the room would be so helpful.

Not seeing it and just guessing…. You can put a bed on each wall with headboards in the corner. L-shaped. Adding a square nightstand to connect the L-shaped beds.

This should give you the floor space that is much needed.

I love the idea of putting the beds in an L shape against two walls. As for colors, you could buy the same patterned bedspread but in each of their favorite colors. Or, favorite color rugs under each bed with neutral (or b&w) bedding. Coordinate that with bold artwork/posters and it could work out really well.

Keeping walls light and neutral will be a good backdop, as in no time they will want a more preteen look and changing a comforter and some accessories will be much easier. Around layout, maybe the boys have a preference.

You could steer clear from their favorite colors altogether and go with a theme that they both like instead. Vinyl stickers are an easy way to do this. Just add the stickers to their room and when their preferences change you change the wall stickers out. Custom Vinyl Decor allows you to choose from a variety of colors for all of their stickers, so if you are dead set on sticking to red and yellow, you could customize your stickers to their colors.

Do they need floor space for toys? My kids are 10 and 12 and are more into books, art, video games and sports now vs toys on the floor. So a bookshelf with storage/display for all the special things kids like to save (like gymnastics ribbons and trophies) could be a priority. If your beds are up on legs, you can store things in boxes underneath. And putting the beds in an L shape could work, or side-by-side with a dresser between (more storage!) if you can sacrifice the floor space.

I love Sabrina's Pendleton blanket idea to incorporate the colors. Or Glo's idea of a shade of the colors vs primary colors; you're going to have teenagers really soon and they might appreciate moodier or more neutral tones. In my experience, kids' rooms get chaotic pretty quickly even if they have a nice foundation, so I'd keep things simple in anticipation of them adding their own special touches.

I like how they used a plug-in sconce for reading to save space and have the bulletin board; each boy could get his own.

Here they put beds foot-to-foot; not sure if you have the space for that.

Just use a frame bed (it can save you a few inches). Use art for the headboards and buy reversible yellow/red comforters. One get the red side and one gets the yellow side. Throw in an area rug...

What about using a neutral main colour and their favourite colours as accents - eg pillow cases, storage cubes, etc

Maybe something similar to this?

…note price as it‘s on clearance. A stripe might be a good choice and navy is a good third color in accessorizing.

I see a trundle bed what is that for? I need a to scale floor plan to really even begin to talk layout In the picrture all I see is a really crowded mess.The floor plan will help. To scale on graph paper showing windows , doorways and all measurements clearly marked. Post here in a comment do not start another post. I ahve no clue we can help with layourt any other way.