it always picks the newest non-full item (or stack) you have in your inventory, then takes the newest full stack of money.
in an ideal world, looking at this picture, you'd want tarkov to use my stacks starting from the bottom right side. after i spend some money, you can see, it does use that stack, because it's my newest non-full one. if i sell an item, in this case a bitcoin, here's the resulting stacks, then since it's the newest (and non-full) stack, you'd expect tarkov to use that stack, and it does.
here's the result after i sell a few more bitcoins to therapist in bulk, which has a full (new) stack in it, and the result, then if i spend that last small stack, ends up like this.
if you stack up your roubles and make a full stack, the resulting stack will not change position, it will stay exactly where it is in the queue, wherever it may be. since there's no way for you to tell what the order of oldest > newest is (as far as i know), if you notice a stack being used out of order, you'll have to move it to the end of your money case, and move all other stacks around to accommodate it.
in its current form, lockdown is complete garbage. it only gives you 13 extra provisions, and in return you only get a 6 point leader in the form of ...