Hello Mike and welcome to Community.
Sorry to hear your having trouble with your Invoice template customisation, would it be possible to post a screenshot of the issues which you are experiencing?
The Custom Form Style option does have limitations to the level of adjustment available for spacing and general layout of invoices, however you can create your own invoice template and layout from scratch with our Import Style feature. To activate the Import Style option first go to the Cog Wheel in the top right of your dashboard and select QuickBooks Labs. Here you will be able to find Import Style here you will also see a video which demonstrates the steps to set a custom invoice.
Please let us know if we can support you any further with your account.