I can't offer much advice without screenshots or further context, but I'll try. When adding materials to the rune, add iron first, as that will give the rest of the build enough stability for everything to stick. Remember, it will always want to start building from the ground upwards, so make sure to add load-bearing and structural components first. Depending on how bad your build is messed up and how big it is, I would probably suggest tearing it all down, removing any unbuilt portions of the blueprint, and then replacing the blueprint and bp rune. Also remember to have all of your crafting stations close enough to the components they are required to build (forge, stonecutter, workbench, etc.).