Hi, I'm enjoying the mod a lot. Currently I got my long awaited dimension folding engine in a hope that through the cube manipulations I'll be able to get more cubes circulating in my base. But I'm starting to be a little afraid of the possibility that I'm required to reach the end goal with only "the one" starting cube. Am I missing something?

You aren't missing anything - optimising cube time is one of the cornerstones of this mod.

If you feel like large parts of the factory are just sitting waiting for the cube to do something, you may need to look at optimising things a bit more so that the cube is inside a machine working as much as possible.

Hmm. In that case I need to rebuild my base from the scratch :( At least now I have more advanced processes available to me.

Maybe, or you need to look at things a little differently - if the cube takes a while to get somewhere, just make it stay there longer making more stuff before sending it back? There's also some tech for moving it around a little more quickly

Though FWIW I just moved it around lines of cargo wagons which is hard to beat for speed

Indeed, this mod requires completely different way of thinking. Even with this restriction I'll try to build the "city cells" rail system where each cell requires cube as an input and is dedicated to build specific item. Am I going to far?
BTW, which tech allows for quicker cube moving?

Theres a tech that unlocks with the blue cards and makes trains carrying the cube move really fast.

I think the city cells would work fine, the magic is in the cube prioritisation and making sure it only goes where it can be used effectively. Stuff that was important for me was making sure there were large input and output buffers and making sure machines could be loaded and unloaded really quickly so I could run the cube multiple times at once before sending it off again. If I couldn't empty the machine in time then I'd set up parallel setups so the cube could be run in those while other machines were emptying.

Sounds like I'm doing many things similarly to you, though there are also some interesting ideas new to me.

I just finished today so I'm hardly an expert, but yeah this mod introduces so many ideas that are really cool and different to vanilla or other mods. I really like how building intricate setups has so much payoff, and the buffering is a tricky mechanic that I haven't seen explored with other mods in the same way.