Any effects that modify a creature’s power and/or toughness without setting them to a specific value (i.e. ones that don’t affect base power and/or toughness) will apply after its base power and toughness are set, regardless of the order those effects were created. The same is true for counters that modify its power and toughness.

Square Up overwrites all previous effects that set the target creature’s power and toughness to specific values. Other effects that set its power or toughness to specific values that start to apply after Square Up resolves will overwrite this effect.