THIS IS HOW I "PREP" OVERALLS for APPLIQUE WORK :
IF I am using o'alls that have a bib pocket, I usually remove it completely.
But this (usually) leaves those nasty stitch-lines & darker areas where the pocket WAS.
So, I either :
1. leave the bib blank & make sure the applique I'm applying covers all "offensive lines & dark areas"

...
but sometimes, that's not always possible.
In this case I will opt to :
2. remove the bib pocket & cover the entire bib with a contrasting background fabric, and apply my applique to the front of the bib on top of that fabric cover.
I seal the fabric down with lightweight wonder-under, + fold over edges & stitch them down.
Depending on the large bib applique, I stop the bib cover fabric at the waistband ~OR~ continue a bit farther down, closer to the front hip pockets
FRONT HIP POCKETS =
the thinner white pockets right under the waistband, by the hips ...
I steam-a-seam them down flat to the inside of the o'all.
Before I stared doing this, I had a couple of pockets fold up on me WHILE I was appliquing over them.
I didn't realize it until it was toooo late, and it was a nasty, lumpy mess =
that had to be ripped out & redone ...
I totally avoid THAT now

FIRST, I turn the o'alls inside out & press them flat (this also "pre-shrinks them a tad, you'll understand when you try it) ...
Then, I use "steam-a-seam" (1/2" wide, comes on a spool) the pocket flat to the inside of the overalls, & pretty much ignore them, after that.
This helps to keep them flat while you work over them from the outside.
Turns out really professional looking
BACK POCKETS = sort-of the same as bib pockets =
Remove the pocket & try to cover with appliques
OR ignore & leave them, as they are.
HAMMER / TOOL STRAPS =
I remove leg straps, IF they don't go with my applique theme.
You can cut them off at the seams they are attached at, but that leaves a bulky seam & back pocket edge ...
IF that does not bother you, leave it like that.
IF that bulky-ness bothers you, you can cut the stitching in those areas and remove the strap bit inside that seam & out from under the back pocket ...
Then, replace the stitching & "Orange" top stitching, as needed, to make it all blend back in & seal the side seam hole.
LEG POCKETS =
those neat little squared-of leg pockets ...
Sometimes, they require too much effort to dispose of, or the results of trying will not look great =
So, generally I ignore the& work around them.
But, IF the appliques can cover it = I remove that pocket & cover that spot.
TO WORK ON THE LEGS EASILY =
Don't forget that you can undo the INSEAM (that's the seam down the insides of the legs).
This way, you can easily work on the legs as flat panels.

!
When you are done with your appliques, replace the inseam ...
Add ruffles before or after you do the inseam = you'll figure out which one's easier for you.
PRE-WASH = Don't forget to TRY to pre-wash your darker overalls,
BEFORE you do appliques.
SOMETIMES, later the denim's darker colors can BLEED BLUE into the appliques & ruffles, in the wash AND/OR even if you hand wash and HANG DRY.
That's about it, right?! Good Luck ... Hope that helps.