Electronic – Power Isolation generating error in KiCAD

I think what I would do here is simply have two global supply names, one for each supply e.g. +5V_A, and +5V_B. Then you can use the standard supply symbols.

OR

Have a master sheet with all the hierarchical sub sheets on it (power supply and driver boards) and wire things up directly using the hierarchical sheet inputs. Here is an example of this (only power net wired for clarity):

Master Sheet:

Individual Sheet:

Individual Sheet with two symbols used (Sheet 2):

PCB connection:

The same hierarchical label (3V) is used on each sheet, but on the master two separate regulators are used. One supplies sheet 1, and the other sheets 2 and 3. On sheet two another IC is also supplied with a separate 3V symbol - on the master sheet you can see two inputs are needed.
The hierarchical symbol does not appear to have automatic connection, so you either have to wire it up normally on that sheet, or add as many input of the same name to that sheet as separate symbols used.
You can on the PCB snapshot (the other net is a normal global ground symbol) everything is connected correctly.

In case this is relevant - if you want to split one supply into two nets, use a "jumper" component (e.g. 0Ω resistor) so the schematic doesn't complain, so then you can have e.g. main_supply, supply_1 and supply_2 all electrically connected, but split for PCB requirements (e.g. like you might have an analog and digital ground)

OR Possibly:

Make a power supply symbol, use the # symbol in the reference designator (IIRC) which tells Kicad it's not a real component. Don't use a power flag on it though - this may work for a local power symbol if the quote below is correct (documentation is not the best though, and is outdated in some places so you need to be careful)

To quote from the link below:

A Power Symbol (VCC, V3P3, etc.) gives the net its name and is used on each page to tie to the global power net. It is a special component not listed in the BOM. A Power Flag (PWR_FLAG) symbol which gives the net its global characteristics - connecting power nets between sheets.

There is info on creating power symbols at the bottom of this link.

Basically all non-trivial layouts will have mathematically guaranteed track crossings, if restricting yourself to a 2D plane. The trick is to not restrict yourself to a 2D plane ;)

Technique 1: Multi-layered PCB. If track A needs to pass to the other side of track B, make it go through a via (an electrically conductive hole in the PCB) to the bottom PCB side, continue there for a bit, and come back up again through a second via on the other side of B. More sophisticated designs even utilize four, six, eight or more layers to make routing possible.

Technique 2: Jumpers. Often you can get away with using parts (resistors/caps/ICs) as bridges. If the part is wide enough, you can make a trace go in between its pads and thus cross the path. If you do not have a part to route under, available where you need it, you can add so-called jumpers (think 0 ohm SMD resistors, or just pieces of wire for through-hole) to jump over existing traces. This solves the track crossing problem without utilizing extra PCB layers, and thus can save costs or time in PCB manufacturing.

Other tricks are for example connecting ICs not outward, but having traces go under the ICs body and continue from there. This can help disentangle the buses leaving thin-pitch ICs.