'normally' is hard to quantify, but I'll give you an answer in the context of a very thin embark.
If you only have one cavern, it will place it just above the highest point of magma. If you don't add any extra separation layers manually, it will be separated by 1-3 layers.
That means, from top to bottom (excluding trees) it will proceed as: the embark layer, then soil layers, then some stone, then the top of the cavern, the cavern, the bottom of the cavern, then at least 1-3 stone layers, then magma layers, then the SMR sea.
Caverns are typically 5 layers thick, inclusive, on a flat embark.
Ultimately, how many layers you want between the soil and the top of the cavern is entirely up to you. "Z Levels Above Layer 1" can be as few as 5, or as many as 100+ stone layers.
if you had three caverns, and each took 5+1, as a minimum including the gap, then you would have 5, +6, +6, then the top of the third cavern. Call it an even 20 as a round number, even though strictly speaking, it could be as little as 17.
This worldgen below has embarks in the southeast edge/corner starting at 149, one soil level 148, then from 147-128 is stone, then the cavern starts at 127, ends at 123 (5, inclusive), then magma starts at 119.
In this case the value of '20' is the 147-128 (inclusive). In other words, change that value "Z Levels Above Layer 1" to whatever you want to simulate the thickness of the other two caverns, and you're set.
worldgen
Created in DF v0.47.04.
[WORLD_GEN]
[TITLE:1CAV-20]
[SEED:J90cZIucIuVDzHLBZwxU]
[HISTORY_SEED:bmOxaMdCCT9mbs70njFM]
[NAME_SEED:DncZ7ibnHSvku1bHFdfs]
[CREATURE_SEED:WVk40qQogqIvylweYlLm]
[DIM:17:17]
[EMBARK_POINTS:0]
[END_YEAR:200]
[BEAST_END_YEAR:200:-1]
[REVEAL_ALL_HISTORY:0]
[CULL_HISTORICAL_FIGURES:1]
[ELEVATION:299:301:0:0]
[RAINFALL:0:0:0:0]
[TEMPERATURE:25:25:0:0]
[DRAINAGE:0:100:3200:3200]
[VOLCANISM:0:0:0:0]
[SAVAGERY:0:0:0:0]
[ELEVATION_FREQUENCY:1:1:1:1:1:1]
[RAIN_FREQUENCY:1:1:1:1:1:1]
[DRAINAGE_FREQUENCY:1:1:1:1:1:1]
[TEMPERATURE_FREQUENCY:1:1:1:1:1:1]
[SAVAGERY_FREQUENCY:1:1:1:1:1:1]
[VOLCANISM_FREQUENCY:1:1:1:1:1:1]
[POLE:NONE]
[MINERAL_SCARCITY:100]
[MEGABEAST_CAP:0]
[SEMIMEGABEAST_CAP:0]
[TITAN_NUMBER:0]
[TITAN_ATTACK_TRIGGER:0:0:0]
[DEMON_NUMBER:0]
[NIGHT_TROLL_NUMBER:0]
[BOGEYMAN_NUMBER:0]
[NIGHTMARE_NUMBER:0]
[VAMPIRE_NUMBER:0]
[WEREBEAST_NUMBER:0]
[WEREBEAST_ATTACK_TRIGGER:0:0:0]
[SECRET_NUMBER:0]
[REGIONAL_INTERACTION_NUMBER:0]
[DISTURBANCE_INTERACTION_NUMBER:0]
[EVIL_CLOUD_NUMBER:0]
[EVIL_RAIN_NUMBER:0]
[GENERATE_DIVINE_MATERIALS:0]
[ALLOW_DIVINATION:0]
[ALLOW_DEMONIC_EXPERIMENTS:0]
[ALLOW_NECROMANCER_EXPERIMENTS:0]
[ALLOW_NECROMANCER_LIEUTENANTS:0]
[ALLOW_NECROMANCER_GHOULS:0]
[ALLOW_NECROMANCER_SUMMONS:0]
[GOOD_SQ_COUNTS:0:0:0]
[EVIL_SQ_COUNTS:0:0:0]
[PEAK_NUMBER_MIN:0]
[PARTIAL_OCEAN_EDGE_MIN:0]
[COMPLETE_OCEAN_EDGE_MIN:0]
[VOLCANO_MIN:0]
[REGION_COUNTS:SWAMP:0:0:0]
[REGION_COUNTS:DESERT:0:0:0]
[REGION_COUNTS:FOREST:0:0:0]
[REGION_COUNTS:MOUNTAINS:0:0:0]
[REGION_COUNTS:OCEAN:0:0:0]
[REGION_COUNTS:GLACIER:0:0:0]
[REGION_COUNTS:TUNDRA:0:0:0]
[REGION_COUNTS:GRASSLAND:0:0:0]
[REGION_COUNTS:HILLS:0:0:0]
[EROSION_CYCLE_COUNT:1000]
[RIVER_MINS:0:0]
[PERIODICALLY_ERODE_EXTREMES:0]
[OROGRAPHIC_PRECIPITATION:0]
[SUBREGION_MAX:5000]
[CAVERN_LAYER_COUNT:1]
[CAVERN_LAYER_OPENNESS_MIN:100]
[CAVERN_LAYER_OPENNESS_MAX:100]
[CAVERN_LAYER_PASSAGE_DENSITY_MIN:0]
[CAVERN_LAYER_PASSAGE_DENSITY_MAX:0]
[CAVERN_LAYER_WATER_MIN:15]
[CAVERN_LAYER_WATER_MAX:15]
[HAVE_BOTTOM_LAYER_1:1]
[HAVE_BOTTOM_LAYER_2:1]
[LEVELS_ABOVE_GROUND:12]
[LEVELS_ABOVE_LAYER_1:20]
[LEVELS_ABOVE_LAYER_2:1]
[LEVELS_ABOVE_LAYER_3:1]
[LEVELS_ABOVE_LAYER_4:1]
[LEVELS_ABOVE_LAYER_5:2]
[LEVELS_AT_BOTTOM:1]
[CAVE_MIN_SIZE:1]
[CAVE_MAX_SIZE:1]
[MOUNTAIN_CAVE_MIN:0]
[NON_MOUNTAIN_CAVE_MIN:0]
[ALL_CAVES_VISIBLE:0]
[SHOW_EMBARK_TUNNEL:2]
[TOTAL_CIV_NUMBER:1]
[TOTAL_CIV_POPULATION:0]
[SITE_CAP:0]
[PLAYABLE_CIVILIZATION_REQUIRED:1]
[ELEVATION_RANGES:0:0:0]
[RAIN_RANGES:0:0:0]
[DRAINAGE_RANGES:0:0:0]
[SAVAGERY_RANGES:0:0:0]
[VOLCANISM_RANGES:0:0:0]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:301:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
[PS_EL:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299:299]
I will note that this world is simply for demonstration purposes.
There aren't any enemies outside of the caverns or aggressive wildlife, and there's only 1 civ.