Either way would work, but I'd be inclined to fit them so the main hose goes to the lower port and the 'joiner' from that to the top port.
My thinking here is that it would help chase the air out.
I have only fitted up one set of these on to a Mini. On that set, I dismantled the Calipers and drilled them internally between the piston spaces, then plugged the upper port. It made for a much neater looking installation.
You are likely on top of it, but if I recall, the threads in these for the hoses are a Metric set up. The threads were M10 x 1.0 and originally, they seal on the nose of the original hose, not with a copper washer like a normal Mini arrangement. The Calipers I've seen weren't machined for a copper washer, they were just the raw casting.
This is the Drawing from the Metro Workshop Manual where they highlight the differences
While I note you have the Goodridge Kit, just me aware too, that while the Hose from a Mini, at 3/8" UNF goes in, they are not the correct fit and can fail as they are 0.5 mm too small. On that, I'd suggest checking the Banjo Bolts you have been supplied with are M10 x 1.0. A simple test here is to try a wheel nut on them and while being close, you shouldn't be able to get it on.