I assume this is what you were looking at:
https://github.com/BelaPlatform/Bela/wiki/Hardware-explained
Bela also provides you with many ways of connecting with the physical world:
Analog In: 8x 16-bit analog inputs at 22.05kHz
Analog Out: 8x 16-bit analog outputs at 22.05kHz
Digital channels: 16x digital GPIO at 44.1kHz or 88.2kHz
Analogue I/O is also software configurable to give 4 channels at 44.1kHz or 2 channels at 88.1kHz
That last part may be useful for you. You can use the audio output channels for 2 channels and the other 3 can be the Analog outputs at 44.1kHz.
For #1) Yes, 3 analog outs makes sense. You will configure 4 channels at 44.1 kHz, and so you can use 3 of them. Make sure your bass/subwoofer channel is one of the analog outputs because you can filter it at a really low frequency, which will let you apply the higher quality CODEC output to channels with more high frequency content.
#2) A couple different ways to do this. One makes sense if you plan to transfer files frequently or if you just want to do it one time.
a) One time, or infrequently. Use SCP. If you're using a computer with a Unix shell then this is easy. With Windows you may need something like PuTTY.
b) (infrequently) USB thumb drive or the flash card with your Bela image. You can partition it and make unused space into a drive that you can read/write from your PC, then mount and access from Bela.
c) If frequently, then connect Bela to the internet and install Samba (apt-get update && apt-get install samba. If you haven't done this before then you will have some time with your friend Google to find a howto for setting up a samba server and shared public folders.
With (c) then you just have a network storage device that you can map/mount over your LAN (which includes the USB connection). Then you can just copy things back and forth as though it is a drive on your main PC.
An extra tip for #1 is to delay the analog outputs to time-align with what comes from 2 channels from the Audio CODEC. The CODEC includes output filtering and oversampling so there is some ~300us delay beyond what the analog outputs have. You will get better audio quality from the analog outputs if you apply a 4rth-order butterworth filter at as low of a frequency as you can tolerate (14 kHz to 18 kHz). This is where the CODECs really shine -- they apply a really steep linear-phase FIR filter and upsample the output so it comes out clean and you don't lose bandwidth. At the same time, even without filtering the analog outputs it will sound ok. The more "hi-fi" you want it the more you will have to filter and what with bandwidth-limiting, filter transient responses and active filter noise you will quickly reach a point of diminishing returns.