It would be done in place of the related adjustments in the original script. In other words, the adjustment would be to the default out of the box table values. I am actually still tuning it a bit. Here is the entire adjustments I am using to the npc_types table. Just remove any sql related to adjusting the stats of the npc_types table in teh original script and use this in its place.
LOCK TABLES `npc_types` WRITE;
-- scale STR up to to hit more frequently
-- UPDATE npc_types SET STR=CEIL(STR*1.2);
-- scale hp/damage down
-- =1-(LEVEL/89)
UPDATE npc_types SET hp=CEIL(hp*(1-(LEVEL/89))) WHERE (LEVEL<81 AND ((id>1000 AND id<800000)) OR id IN ('635','636','646','649','650','667','668','669',' 673','676','677','679','679','679','680','681','82 9','923','924'));
UPDATE npc_types SET maxdmg=CEIL(maxdmg*(1-(LEVEL/89))) WHERE LEVEL<81 AND ((id>1000 AND id<800000) OR id IN ('635','636','646','649','650','667','668','669',' 673','676','677','679','679','679','680','681','82 9','923','924'));
UPDATE npc_types SET mindmg=CEIL(mindmg*(1-(LEVEL/89))) WHERE LEVEL>20 AND LEVEL<81 AND ((id>1000 AND id<800000) OR id IN ('635','636','646','649','650','667','668','669',' 673','676','677','679','679','679','680','681','82 9','923','924'));
-- scale spell and heal down
UPDATE npc_types SET spellscale=50 WHERE level>19 AND ((id>1000 AND id<800000) OR id IN ('635','636','646','649','650','667','668','669',' 673','676','677','679','679','679','680','681','82 9','923','924'));
UPDATE npc_types SET healscale=50 WHERE level>19 AND ((id>1000 AND id<800000) OR id IN ('635','636','646','649','650','667','668','669',' 673','676','677','679','679','679','680','681','82 9','923','924'));
-- adjust agro radius down
UPDATE npc_types SET aggroradius=CEIL(aggroradius*0.30) WHERE aggroradius>20;
-- scale resists down
UPDATE npc_types SET MR=CEIL(MR*(1-(LEVEL/89))) WHERE LEVEL<81 AND ((id>1000 AND id<800000) OR id IN ('635','636','646','649','650','667','668','669',' 673','676','677','679','679','679','680','681','82 9','923','924'));
UPDATE npc_types SET CR=CEIL(CR*(1-(LEVEL/89))) WHERE LEVEL<81 AND ((id>1000 AND id<800000) OR id IN ('635','636','646','649','650','667','668','669',' 673','676','677','679','679','679','680','681','82 9','923','924'));
UPDATE npc_types SET DR=CEIL(DR*(1-(LEVEL/89))) WHERE LEVEL<81 AND id>1000 AND id<800000) OR id IN ('635','636','646','649','650','667','668','669',' 673','676','677','679','679','679','680','681','82 9','923','924'));
UPDATE npc_types SET FR=CEIL(FR*(1-(LEVEL/89))) WHERE LEVEL<81 AND ((id>1000 AND id<800000) OR id IN ('635','636','646','649','650','667','668','669',' 673','676','677','679','679','679','680','681','82 9','923','924'));
UPDATE npc_types SET PR=CEIL(PR*(1-(LEVEL/89))) WHERE LEVEL<81 AND ((id>1000 AND id<800000) OR id IN ('635','636','646','649','650','667','668','669',' 673','676','677','679','679','679','680','681','82 9','923','924'));
UPDATE npc_types SET Corrup=CEIL(Corrup*(1-(LEVEL/89))) WHERE LEVEL<81 AND ((id>1000 AND id<800000) OR id IN ('635','636','646','649','650','667','668','669',' 673','676','677','679','679','679','680','681','82 9','923','924'));
UNLOCK TABLES;
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