Hello @peaces ,
Sorry for my delayed answer!
We cannot increase the "Number of commands" values because, according to the Manual, "Every CFIFO and RFIFO, including CFIFO0, has four entries."
But having a look at the screenshots you've provided, it looks like you are using only a single block of EQADC Push Command, probably with 4 commands, each one ending in a different result buffer. What you can do, is to use multiple EQADC Push Command blocks, each one inserting 4 commands in a different CFIFO and each command to store the results in a different RFIFO. Basically, you can convert 4 values using CFIFO0 to RFIFO0, the next 4 using CFIFO1 and RFIFO1, and so on. Of course, you have to enable the CFIFOs in the ADC Config block.

Please have a look at the attached model.
For the FreeMaster, you can try using the interrupts mechanism. For that, you have to open the FreeMaster config block, and select short or long interrupt (in long it will handle all the data FreeMaster data transfer) with an increased priority higher than the RFIFO interrupts.
Hope this helps,
Marius