Carlos,
That is correct - the switch that has the lowest root priority is the root for those vlans.
What you can do is change the priroity for those vlans eg:-
In 99.254
spanning-tree vlan 7,9,11,12,99 priority 28672
In 99.253
spanning-tree vlan 7,9,11,12,99 priority 32768
In 4507
spanning-tree vlan 7,9,11,12,99 priority 20480
This will make switch 4507 the root for vlans 7,9,11,12 & 99 - switch 3560 99.254 will be the root for all other vlans and secondary for vlans 7,9,11,12 99, and 99.253 will be secondary for all over vlans.
HTH.