Calculation of noise in Non inverting Op-amp circuit
Input is signal frequency is 100Hz. I want to use the 6.5nV/sqrt(Hz)
  but it seems to be a spectral density, and I can't add it to a voltage


This is where the bandwidth of the analog system comes in, the max bandwidth determines the noise. Let's say it's an ADC with a low pass filter at 1000Hz. The ADC would see:

(1000Hz)^(1/2)*6.5nV/sqrt(Hz) = 2.05uV-rms

If the total bandwidth is 100Hz then

(100Hz)^(1/2)*6.5nV/sqrt(Hz) = 0.065uV-rms

In addition, the low pass filter on the input only stops noise contribution from the input, the amplifiers bandwidth is not restricted. It is usually best to low pass filter the amplifier for noise purposes. 

If you get below the 1uV-rms line for total noise, contributions from resistor white noise starts to become significant and needs to be analyzed.