Both setups may work. Which is better is governed by capacitor values, their ESLs and the power delivery network downstream.
In the left-hand setup, the PDN should provide low impedance path at lower frequencies. This is the requirement for this setup to work.
The potential advantage of paralleling two capacitors is lower power impedance in a broader range (assuming 0.1 uF and 10 uF cover different frequency ranges). As for the notorious anti-resonance of the two capacitors - look at impedance frequency curves. The situation when it happens is when one capacitor is still capacitor and another one is an inductor. This should not be the case. So, the answer provided by Spehro makes sense as well.
As for the right setup, it may work also. But note that C1 is the only one to provide power when the bead is closed - so its responsibility is huge. The left larger capacitor may not be needed in close proximity (as assumed by the pic I guess). If the bead closes early (say in units of MHz or tens of MHz), then it should provide low impedance path at kHz (or units of MHz) frequencies where location requirements are relaxed (as light wavelength is on the order of tens of meters at these frequencies). But it depends.
Appendix
Below are some general considerations re ferrite beads that might be interesting.
Consider for simplicity the setup with only one capacitor. The main purpose of the second capacitor in the pi setup is to provide low impedance to power at lower frequencies: