Are these circuits equivalents (caps in parallel with VCC)
In an ideal world they are equivalent. C1 and C2 are parallel in A and in B

A however has its 0.1 µF capacitor physically closer to whatever you are trying to power, so from a decoupling perspective. A is ever so slightly better, judging by the PCB layout.

If possible, put the 0.1 µF capacitor as close to whatever you are trying to power. Literally 1-5 mm away from the pins of your IC. 

Sidenote:
If you want to make it correct, then you should not use ground wires as you've done in both A and B. You got an entire layer of copper clad. Make use of it. 

You will pay the same money for removing 10% copper of the board, or 90% of the board. But if you remove 90% of the copper then that means you probably got thin wires, this is worse and you're doing it with zero gain. Make your traces as wide as you can. Especially regarding your ground.