Once you have put STX tokens in a vault, they have the potential to be earning a yield. The yield comes from Proof of Transfer (PoX in short). You can read more about Proof of Transfer here: https://community.stacks.org/pox
In other words: each vault that has STX collateral has the option to earn a yield through PoX or not. This is binary. Either a vault is stacking or it is not.
Note however that multiple deposits in a vault require you to re-initiate stacking in PoX for the newly deposited STX to be stacked as well. Re-initiating the stacking means that the additional STX will get included in the next Arkadiko cycle. Each Arkadiko cycle is 3 PoX cycles long (approximately 6 weeks).
The reason for this limitation is that once a PoX cycle has started (and there is always one that has started), we cannot automatically add your newly deposited STX to PoX, since that stacking window has closed. This is currently a limitation in PoX and might be solved in the future with continuous stacking.
IMPORTANT: your yield is tied to your vault. Closing your vault before you received or claimed your STX yield means those STX tokens will be lost! If you are waiting for yield, do not close your vault yet. You can pay off USDA debt and still receive yield though.