I have Kali Linux on my pi3. I got two doubts:
1) How do I make vnc to run during boot?(Using ssh) 2) After booting up how do I use VNC using my phone via the USB cable?
You need three things
x11vnc. That's a vnc server which makes you access the normal desktop your Raspberry Pi shows on the HDMI. Other VNC servers open another in-memory desktop instead. Start it in /etc/X11/xdm/Xsetup to have the X11 login available through VNC. You can also start it later, of course.
An Android VNC viewer app. There are numerous.
adb. That's needed for setting up a network connection through the USB cable. It's rather slow so you may want to think again about this.
(Nothing of this is specific to the Raspberry Pi, so your question is off-topic here.)
Best answer is to install raspAP available in github and use raspberry pi hotspot to make connection and then use official vnc server by real vnc setup by
sudo apt-get install realvnc-vnc-server
and download vnc viewer from play store(blue color logo amybe first result by searching vnc viewer) on mobile.
Short answer but hope it helps...