As a disclaimer, I'll admit I have not experimented with the Skychief loading system yet, although it is on the "to do" list. However, I have a suggestion that may (or may not) work for you.
I have a tin cup which I bought from Dixie Gun Works several years ago. It's a big 'un, about four inches broad and four and a quarter high. When I'm at the range and there is not a table handy, I thread my belt through the handle so the cup is at my waist. I use it mostly to hold dirty cleaning patches, but I've seen N-SSA competitors do the same thing with a large tin cup for holding empty loading tubes. I had intended to use the cup for holding greasy wads when I start experimenting with the Skychief load, but just haven't done it yet. My range time is limited, and I usually bring a rifle. Anyway, this ought to keep the wads from contaminating your pouch with grease, and should keep them accessible. On the downside, the open cup won't protect them from rain or debris falling from above, and if you trip and fall they will probably spill out.
This is the cup that I have:
Big Tin Cup from Dixie
The photo on that website is accurate. The cup will look somewhat tarnished when it is received, just as in the photograph. The product description tells us up front that it leaks, but I'm not sure I would want to drink out of it anyway. I think these come out of humble tinsmiths' shops in India, Pakistan, or thereabouts, and without knowing more about its provenance I'm reluctant to use it for beverages. However, it works great for holding non-comestible/non-potable odds and ends on the range or workbench, it looks very "period," and at six bucks I would say the price is reasonable.
On this topic, one other item I've been thinking of making is a "grease horn." One of these is shown hanging from the belt in this picture from
The Ashley Book of Knots, between the marlinspike and the sheath knife:
View attachment 227928
I think a similar horn is shown in a photograph elsewhere in the book. In any event, the grease horn appears to be a short section cut from the large end of a cowhorn, with a wood (?) base fitted into the bottom, and an extension or lobe projecting from the upper rim with a loop of cord or thong to suspend it from a belt. Ashley considered it an essential item for an old-time rigger aboard ship, for holding tallow to grease strands of rope. I have also read that sailmakers kept their needles in the grease horn, shoved down into the tallow to keep them handy but out of trouble. I don't see why a grease horn like this wouldn't work for a muzzleloading shooter, as a holder for small, greasy items like wads. Making one of these might be an interesting project, and a good way to use a horn with a spoiled tip, if you happen to have one.
Best regards,
Notchy Bob
