Instead of the liquied you can request the ingredients, similar to one time logistic requests on a planet.
Open a fuel chemical plant, with q pick up the ingredient e.g. iron ore and then rightclick or capslock leftclick to request Ingredients in that slot. It automatically get set as missing ...

Currently, upgrading a cargo wagon with filters only adds new slots without filters, and I don't think that will change. E.g. for a construction train with 10+ different filters, upgrading from common (40 slots) to uncommon (50 slots) makes it impossible to determine what the 10 new slots should ...

I think that's a workaround for the problem, not a convenient solution. It means that after a flush, all connected pumps need to be manually checked and flushed as well — and as shown in the picture, there can be many of them and/or spread out across a base.

A more convenient solution would be for ...

TL;DR
Add train capacity-based wait conditions to make schedules work cleanly with mixed fluid/cargo trains across different wagon qualities.

What?
For my uranium mining outpost, I run trains that deliver sulfuric acid and pick up ore — one schedule, two conditions: fill fluid on the way out ...