Am i performing Sinesweep correctly? I am bit unsure whether i am doing i sine sweep correctly. 
I am feeding my system a sine wave with f hertz within a given time interval and log its output. 

And then i do the same for another frequency. 

I tried this technique but seem to do it incorrect or so i think.
I tested for 2 frequencies, and fed them into  Ident in matlab and got a fit rate of 98 % which makes no sense that it could build a such a good bode plot based on 2 values.. 

I am doing something wrong.. should it not have more than one 2 input or is it enough?
The theory behind sweep-sine measurements of LTI systems requires a signal with constantly changing the frequency. You cannot simply playback few tones - the whole frequency range is necessary.

So that if you want to identify your system with the impulse response $h[n]$, you feed the sweep sine signal $s[n]$ into it and record the output. Obviously output will be given by the convolution:

$$y[n]=h[n]\star s[n]$$

In order to obtain the impulse response of the system, it is required to convolve the output $y[n]$ with the inverse filter $f[n]$. Generally, the inverse filter is a sweep signal, inverted in time and with scaled amplitude. So in the end:

$$h[n]=y[n]\star f[n]$$



There are two major types of sweep signals: linear and logarithmic (exponential) frequency change. The latter one is more commonly used, since its spectrum is similar to a pink noise. Personally I always use the logarithmic sweep sine:

$$s(t) = \sin\left[ \dfrac{2\pi f_1 T}{\ln\left( \dfrac{2\pi f_2}{2\pi f_1} \right)}\left(e^{\dfrac{t}{T}\ln\left(\dfrac{2 \pi f_2}{2\pi f_1} \right)} -1\right) \right]$$

where:

$f_1$,$f_2$ - initial and final frequency of a sweep

$T$ - sweep duration in seconds

There is no strict rule on what should be the length of a sweep. For example in acoustics, the rule of thumb is that it should be at least as long as predicted reverberation time. 



For more literature on the topic, please refer to the following sources:


  Meng Q., et al. - Impulse Response Measurement With Sine Sweeps and
  Amplitude Modulation
  Schemes
  
  Farina A. - Advancements in impulse response measurements by sine
  sweeps
  
  Farina A. - Simultaneous Measurement of Impulse Response and Distortion with a Swept-Sine Technique