OK, I might be completely off the mark here since this is a bit out of my league. If so, please correct me. But this is how I see it:
First of all, why do we need padding and alignment at all? It's just wasted bytes, isn't it? Well, turns out that processors like it. That is, if you issue an instruction to the CPU that operates on a 32-bit integer, the CPU will demand that this integer resides at a memory address which is dividable by 4. For a 64-bit integer it will need to reside in an address dividable by 8. And so on. This is done to make the CPU design simpler and better performant.
If you violate this requirement (aka "unaligned memory access"), most CPUs will raise an exception. x86 is actually an oddity because it will still perform the operation - but it will take more than twice as long because it will fetch the value from memory in two passes rather than one and then do bitwise magic to stick the value together from these separate accesses.
So this is the reason why compilers add padding to structs - so that all the members would be properly aligned and the CPU could access them quickly (or at all). Well, that's assuming the struct itself is located at a proper memory address. But it will also take care of that as long as you stick to standard operations for allocating the memory.
But it is possible to explicitly tell the compiler that you want a different alignment too. For example, if you want to use your struct to read in a bunch of data from a tightly packed file, you could explicitly set the padding to 1. In that case the compiler will also have to emit extra instructions to compensate for potential misalignment.
TL;DR - wrong alignment makes everything slower (or under certain conditions can crash your program entirely).
However this doesn't answer the question "where to better put the padding?" Padding is needed, yes, but where? Well, it doesn't make much difference directly, however by rearranging your members carefully you can reduce the size of the entire struct. And less memory used usually means a faster program. Especially if you create large arrays of these structs, using less memory will mean less memory accesses and more efficient use of CPU cache.
In your example however I don't think there's any difference.
P.S. Why does your struct end with a padding? Because arrays. The compiler wants to make sure that if you allocate an array of these structs, they will all be properly aligned. Because array members don't have any padding between them.