It seems like this question on unix stackexchange might provide some insight.
I'm just gonna copypaste the content from there, since I don't see how to improve upon the answer given, and since I cannot mark as duplicate as the question exists on a different exchange. Based on Krita's documentation, the configuration seems rather limited when it comes to choosing input devices, so you might have to go for the latter option of multiple pointers.
So here's derobert's answer:
Personally, I found it easier to leave it the way you currently have it, especially with switching GIMP to single-window mode. But I only randomly play with my Wacom tablet, not use it seriously. That said:
Don't affect the pointer
You just need to use
xinput to float the inputs that you don't want to move the core pointer (mouse pointer).
Here is what xinput looks like with my Bamboo tablet:
anthony@Watt:~$ xinput list
⎡ Virtual core pointer id=2 [master pointer (3)]
⎜ ↳ Virtual core XTEST pointer id=4 [slave pointer (2)]
⎜ ↳ Logitech USB-PS/2 Optical Mouse id=9 [slave pointer (2)]
⎜ ↳ Wacom Bamboo 16FG 6x8 Pen stylus id=11 [slave pointer (2)]
⎜ ↳ Wacom Bamboo 16FG 6x8 Finger touch id=12 [slave pointer (2)]
⎜ ↳ Wacom Bamboo 16FG 6x8 Pen eraser id=14 [slave pointer (2)]
⎜ ↳ Wacom Bamboo 16FG 6x8 Finger pad id=15 [slave pointer (2)]
⎣ Virtual core keyboard id=3 [master keyboard (2)]
↳ Virtual core XTEST keyboard id=5 [slave keyboard (3)]
↳ Power Button id=6 [slave keyboard (3)]
↳ Video Bus id=7 [slave keyboard (3)]
↳ Power Button id=8 [slave keyboard (3)]
↳ USB-TMU-V3 id=10 [slave keyboard (3)]
↳ AT Translated Set 2 keyboard id=13 [slave keyboard (3)]
As you can see, the Wacom tablet shows up as a bunch of different pointer devices. The 'pen stylus' and 'pen eraser' are the two from the pen; 'finger touch' is using it as a touchpad; 'finger pad' is the mouse-like buttons on the tablet itself (not the pen).
To float one, just use
xinput float «id». E.g.,
xinput float 11; xinput float 14 would make the pen (both stylus and eraser) no longer move the mouse pointer.
Next, you'll have to go to GIMP's Preferences, Input Devices, Configure Extended Input Devices and configure GIMP to handle the stylus and eraser. Similarly, you'll have to configure Inkscape, etc.
An alternative thing you can do with
xinput is to create a second (third, etc.) "master", and attach the input devices there. Then you'll have multiple mouse pointers. Not all apps know what to do with this.
anthony@Watt:~$ xinput float 12
anthony@Watt:~$ xinput create-master 2nd
anthony@Watt:~$ xinput list
⎡ 2nd pointer id=16 [master pointer (17)]
⎜ ↳ 2nd XTEST pointer id=18 [slave pointer (16)]
⎣ 2nd keyboard id=17 [master keyboard (16)]
↳ 2nd XTEST keyboard id=19 [slave keyboard (17)]
xinput reattach 12 16