Hello,
I haven't receiving yet my digispark boards, then, maybe i do a mistake, but as far as i know you can use Putty or whatever serial console you want for debugging.
For the other port i think yes.
But i stay surprise by two things.
Why you want stuck a Pin and use 'softwareserial' library on a wireless project ? Unless in debug mode, the softwareserial library need wiring to another device to work, no matter it's in RX or TX only.
Why you want to use the 1Hz clock signal for accurate the millis() or micros() as you have the time on your RTC through the I2C bus ?
Unless the code is too heavy to transform a date/time reference from the RTC in a 'long'. Otherwise you can do the same it's in millisec also. It's also timer in RTC, more stable, but timer.
In any case your code interesting me to study it, if it's not too much demanding that you will share it, thanks
Regards