I have a .54 Lyman percussion rifle. I was wondering if it was feasible/safe to use multiple patches in order to shoot a smaller ball for squirrel.

Personally, if you're thinking about getting to a ball small enough not to do a lot of damage to edible parts, you'd probably have to go all the way down to a .32 and I can't imagine it would be accurate;
In addition, multiple patches may allow a ball to slip/move forward, etc.

Onesuggestion would be to sight it in with a throttled back load like 40grns of powder, and just go for head shots, or dead center in the middle so no major edible parts are damaged....I do that witha .45cal I use for squirrels

I agree with Roundball.. if small game is on the menu, then lower the powder charge and work up a light load. No matter how small a caliber you go down to you are going to have to go for a head shot or non-meat area shot so keep the same caliber and work up a accurate light load. Head shoot them.

In order to produce accuracy, the patch/ball combo has to be tight enough that the pattern of the patch eweave is engraved ontop the ball, and the land marks must also be visible. The smaller the ball and the thicker the patch (or in yoiur case, patches), the less likely this is to be true, and the more gas will blow around the ball through the patching material.

I suggest you "bark" your squirrels, rather than try to use a ball that is too smal to be accurate. "Barking" is what D. Boone, et al did-you shoot into the tree limb or trunk just under the squiurrel. Either the shock from the close impact or the fall will kill it!