What is it exactly that you are trying to accomplish?
The Boot0/Boot1 pins control where the processor begins executing code from. The exact options vary from one STM32 type to another, but generally you can boot from:
Main memory: This is for starting in on-board flash (most commonly used)
System memory: On-board bootloader in ROM
Exact functions vary with the device and bootloader revision, you should refer to ST AN2606 for details, it lets you do things like bootstrap flash from UART, boot from I2C, SPI etc.
SRAM: This is used to run code you have previously loaded into SRAM, possible uses:
Load code via hardware debugger, then reset & run.
Load code via download protocol from bootloader then reset & run (you can also run directly from bootloader, but if you want it to "cold start" the code this would do it).
Load code via application then reset to "cold start" it.
If you are writing a custom bootloader, then it will most likely reside in main flash and you would boot it using "Main memory". It would then look after launching the application, and providing whatever other services you need (secure updates etc.).
The only time you might boot otherwise would if your bootloader got corrupted and you need to reflash it (assuming the smaller MCU has this capability). What you do with Boot1 would depend on what you implemented to accomplish that, and what it means on the particular STM32 variant that you are using. For the STM's I use Boot1=1 means to run the on-board bootstrap ROM, Boot1=0 means run from SRAM. To recover the system via the bootloader you need an external source to bootstrap an image from (UART, I2C, SPI, USB etc.), To recover from SRAM you would have to have a way to place bootstrap code there first (debugger etc.) and also a way to feed the application image to it as it re-installs it.
If your design does not include the capability to recover the bootloader in the larger MCU, then just tie off Boot0 to always boot from main flash (Bootloader would have to be recovered via debug interface).
Dave