You can use the full size of the device if the ROM is in the stock slot.
If the ROM is not currently in the stock slot, you certainly have the option of backing it up and restoring it to the stock slot. You can delete the alternate slot(s) as soon as you have made the backup successfully.
If you are low on space the you will want to make the backups to the external SD card.
If you have lightly-rooted stock in the stock slot (a good idea IMO), make a backup of that too, and make sure you have copies of these backups off the device. (On the ext SD card at a minimum, on a PC even better).
Note that if you wanted to resize an alternate slot, you can use the exact same technique:
- delete slot
- generate new slot of desired size
- restore into the newly created slot.
Maybe it's just me, but if you are asking this question it suggests little practice at making backups and restoring them. You should be making backups somewhat regularly.
"I'm gonna start coding placebo apps. That way I will be sure that the complaints are real and the praises hollow."