How to organize large Rails application

If you're just learning Rails, I'd go with the Rails way ("When in Rome, ..."). If you're worried that your startup may falter due to scalability issues down the road, I'd suggest you revisit your decision to use RoR. Solving scalability problems is hard enough in an environment you know well, you don't want to struggle with an unfamiliar one when you're under the gun. (Note that this isn't particular to Ruby, it's just as applicable to Python, Scala, Perl, C++ or any other language you don't know...)

I'd recommend the behaviour driven development pattern,

If your not familiar let me give you an overview:

Start at the nuts and bolts the "elevator pitch" of the application..

"What is this thing we're building? What value does it bring?"

And then pick the absolute minimum requirement "feature" and start "specing" it out.. id' recommend using Cucumber: http://cukes.info/ and Rspec: http://rspec.info/ to describe the feature how it must behave.. run the tests/specs and watch them fail..

Then dive in and start implementing the feature and watch the tests pass 1 by 1..

When this feature is done (all the tests pass) repeat the process.. move onto the next minumum requirement "feature" and so on..

As for the workload focus on the feature your building together, the programmer works on the behaviour and the designer works on the look and feel until both work perfectly together..