Rob I guess I am a little confused. With the enolmatic cartridge filter the vacuum suck all but about a cup out of the cartridge vessel. That I just dump into the last bottle with a funnel. I also do that in between wines, but I do not clean or rinse the filter between wines. I just start with the whites then go to the reds.
After running k-meta through the system before bottling I empty anything left in the vessels but leave the filter in tack. I fill two bottles and dump them back in the carboy with the wine. These two bottles will have a heavier concentration of K-meta from the filter and this way they are just put back in the main carboy to blend.
I hope this makes sense to you. I have not used the whole house filter but I am assuming it is the same way. This is way easier then using the mini jet, especially since you can filter and bottle in one step.