Hercules TMS570LS1224 ADC Halcogen configuration

what is that cycle time?? What does it do?? is the sampling time for the ADC??

Cycle time is the period of the ADCCLK. The ADCCLK is the reference clock by which it uses to operate the conversion. See below description about the sample window from the TRM. SW is the sample window which is also named sample time in the HalCoGen GUI.

Group1 Acquisition Time. These bits define the sampling window (SW) for the Group1 conversions.
SW = G1_ACQ + 2 in terms of ADCLK cycles.

a) The FIFO size. If im going to only use those 6 channels, should I just write 6 in there?? because thats what the message says when putting the mouse in there (BTW it has a typo

If you want to generate interrupt to the CPU after six channels are converted then you should put 6 as your FIFO size.

b) What could work better for me? Use a continuous conversion and read the data every timer compare? or just call the START_CONVERSION function from timer compare and wait for the data to be ready on GROUP1 interrupt and STOP_CONVERSION?? 

Both methods are provided. I guess you need to experiment with both to see which one suits your application. I will suggest starting with the adcStartConversion() first for better control.

c) About the ID. Why do I need that?? The ADC doesnt go from channel 0 to channel N?? or the scanning is random? I saw on the example that it was used adc_data[0], so I assumed that the ADC scans all the pins and save the data on the corresponding location... If the ADC actually saves the data from channel 0 on [0] and channel 1 in [1] why would I need the ID?? 

No, your understanding is not correct. Let's say the channels you want to convert are 10,11,12,13. The channel 10 will be save in adc_data[0] while channel 13 will be saved in adc_data[3].

d) If using continuous conversion for both, Group1 and Group2 is possible for what I read on TMR, but just to make sure I understand: The Group1 is high priority compared to Group2, so first convert Group1 and when finishes all the channels, starts with Group2 right?

Yes, your understanding is correct. All channels in Group1 will be converted first before moving to Group2. See below excerpt again.

Any of the available analog input channels can be assigned to any of the conversion groups. This also
allows a particular channel to be repeatedly sampled by selecting it in multiple groups. There is an
inherent priority scheme used when multiple conversion groups are triggered at once. The Event Group is
the highest-priority, followed by the Group1 and then the Group2.

Here we have the memory configuration. BNDA corresponds to Group1? or for Group event?? What this part does?? what is BNDA and BNDB?? why 2*N there?? Im guessing 64 is the maximum words I can save inside the FIFO right??

0 to BNDA corresponds to the size you allocate for the Event group. BNDA to BNDA corresponds to the size for Group 1. BNDB to BNDEND corresponds to the size for Group 2.

I read on TMR that when FIFO is full, a flag is turned and I have to reset FIFO right? but I could reset it every time I get the data no?? of FIFO is cleared when using adcGetData()???

Can you quote from the TRM about the FIFO full? I don't understand the question.