Hi Dennis, you should be able to program your flash while running u-boot or Linux kernel. This is probably the simplest method you can have.
If you need to program your flash before you have any software running on your board you need to access your flash and/or your SoC through an interface and JTAG is then pretty much the only option you would have but then you would need a JTAG debugger. Is this not what you like to do ?