I assume your are talking about using a secondary for bulk aging and ideally you brew enough beer to fill the secondary vessel you will be using.
You can also do the following
1. Bulk age in primary, the headspace has already been flushed of o2 by fermentation. The autotalysis police will show up to comment on this but I have had beer sit on yeast for 6 months with no issue and I know there are others on this forum that have gone longer.
2. Use a keg for bulk aging, you already know how to flush that head space of co2
3. If you are going to use a secondary that you cant conpletely fill...
Turn off the gas at your regulator, unscrew the mfl from your gas disconnect
Sanitize the hose and put it into your secondary.
Turn the gas on for a short time
Then rack the beer in.
C02 is generally heavier than air and you should have a nice cushion of c02 when you are done racking.