I'm considering using this mod in my next gameplay. Will those charge packs replace automatically, if you have spare ones in the inventory or do you have to change them manually?

At the current time, the charge packs need to be swapped manually when they discharge.
A feature for auto-swapping is something I have considered.
I will have a look at that. It would likely be an additional research to "enable" it

Keep in mind, they are lower priority than normal batteries. So you can place in Chargepacks to charge batteries in the suit.

I've actually checked this and there is no need for automatic replacement. If you have full equipment grid, then you just need to CTRL+click empty charge packs and CTRL+click on stack of charged ones to quickly replace them, new ones will automatically fill all the empty spots in the grid.