Go to WhatsApp - Settings - Chats - Backup, and see how much space Whatsapp is trying to upload (you can choose to not include videos to reduce most of the size)
Now, there are 2 Whatsapp backup switches to handle, they are both on by default, hence, by default, WhatsApp is an odd and inconvenient outlier since (compared to iCloud Photo library) it literally duplicates the space required if both switches are on, let me explain:
1st switch: iPhone Settings app > Tap your name in the top > iCloud > scroll down to see the switch (this switch creates a live backup that allows for an independent backup, meaning you don't need to restore your whole iphone to restore this backup, you can delete Whatsapp Only and said backup will be detected when you reinstall Whatsapp). You get to pick your frequency
2nd switch: iPhone Settings app > Tap your name in the top > iCloud > Manage Storage > click "Backcup" green icon row > Click your device > here you have a list of your TOTAL apps, each might save a tiny bit of settings info for each app (not the app itself), this is a packaged backup that also saves your downloaded app list (no matter if you switch off every app). So, Here you see WhatsApp too (2nd switch) <- if on, Whatsapp backup will take 2x space of your total iCloud space. As I understand, this backup can only be accessed if you restore the whole iPhone (whole package see).
Post-context: for years, I've turned off the 2nd switch with no problems. But ever since iOS 13, background activity is a mess for Whatsapp, and even though I have more than enough space, auto-daily Whatsapp backup is not happening. I now have the question if I can invert the switches, and still be able to access WhatsApp backup by only deleting and reinstalling the whatsapp app, not the whole iPhone. This question arises since the packaged backup (2nd switch) for the rest of the apps (including WhatsApp) works flawlessly, daily, perfectly fine.
TIP:: It doesn't matter if you have iCloud Photo library on on both sections, Apple is smart about this and only backcups once (only takes space one time), that's why I say WhatsApp is an inconvenient-odd outlier when it comes to both switches management.
With all this, maybe your backup is stuck since you have a 2.5Gb Whatsapp backup to be uploaded, which (if both switches on) requires 5Gb of free space. <- but in my case, not even having the double free space does the trick, auto-backup is not happening.
Best Answer
Deleting one does not affect the other as they are backups of different types.
The backup in iCloud Backup (first screenshot) is a backup of the contents of the app container on your iPhone. This is backed up every night as your iCloud Backup takes place, or manually when you Back Up Now.
The ‘backup’ in iCloud Storage (second screenshot) is a backup created by WhatsApp using WhatsApp Settings → Chats → Chat Backup. This is backed up at most per the interval set in WhatsApp settings, or manually when you Back Up Now.
It is up to you which backup you choose to keep. Personally I would use WhatsApp own backup service with iCloud rather than iCloud Backup.