There are a few primary differences between the two versions of Madcow.
Most notably, the Advanced version skips Wednesday squats after week 4, resulting in 2 squatting days per week instead of 3.
The Advanced version also has two main blocks: one higher volume, the other lower volume and higher intensity.The Advanced version programs a new 5RM (+5lb or +2.3kg) at the end of week 4, adds a deload on week 5, then programs a new 3RM at the end of the next 4 week cycle (week 9). The Intermediate version provides a 3 week “ramp” before also hitting a new 5RM on week 4, then just continues adding weight with each subsequent week, indefinitely.
If weekly progress can be made, then the intermediate version is probably more appropriate. When stalling and resets become frequent, then trying the Advanced version may be worthwhile.