I have done a project like this, where the USB is communications link from
an embedded device to be plugged into a PC, similar to using RS232 in the
good old days.  Meanwhile, the device operates on its own, whether its USB
is attached or not.
.
For keeping the power supplies separate, just don't connect anything to the
USB connector's pin 1.  They have a common ground, but the power supplies
are separate.  If you think something may take its power from the that USB
jack, then you are confusing hosts and devices, and several large
dissapointments are headed your way.  We'll assume not, and that this thing
really is a device.
.
As to sensing when it's connected, this is not done by detecting power
supplies, but rather by detecting that one of the data lines has been pulled
up.  (Can't find which right now, but I believe it is D+).  These lines are
normally pulled low.  When the cable is plugged in, one of the lines goes
high.  You connect a 100K resistor from that line to one of the PIC I/O port
pins.  The firmware watches for that pin to change state.  The source code
has a #define that lets you say which port pin you used for this.
.
One more firmware note.  This may have changed in later releases, but the
USB firmware I got sat in an infinite loop waiting for the connect to
happen.  Needless to say, the rest of the firmware was hung until that
happened.  It was an easy enough matter to change the code so that it polled
for that connection in my application's main loop instead.  Just something
else to watch for.
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