Descriptions like that do not have useful information for us to help you. I guess you miss some fundamental concept in PCB design and to find out what part it is that does not work we need more information about your nightmares.
With prototypes it’s common to make a few bodge wires to get the PCB to work. It looks ugly, but the electrons don’t care and when done properly it also does not have averse effects. It’s even common to see bodge wires in the first production runs of commercial products. For the next production run it is of course more cost effective to make a new revision of the PCB, but a few faulty connection is no reason to throw away the PCB’s.
KiCad also has the ability to: