You can actually add more encounter types instead of replacing any; to do this you have to edit both worldmap.txt and worldmap.msg.
First to add the encounter type, look through the "Newly added random encounter types" table, the entries should look like this:
[Encounter: NAV_Enclave_Patrol]
type_00=pid:16777466, Item:395(wielded), Item:721, Item:(0-50)41, Item:(1-5)545, Script:794, If(Rand(10%)) ; Enclave Patrol male w/ Vindicator Minigun and 4.7mm
type_01=ratio:20%, pid:16777466, Item:24(wielded), Item:(0-50)41, Item:(0-1)38, Script:794 ; Enclave Patrol male w/ Plasma Pistol and Small Energy Cell
type_02=pid:16777466, Item:582(wielded)), Item:722, Item:(0-50)41, Item:(0-1)545, Script:794, If(Rand(10%)) ; Enclave Patrol male w/ H&K G11E and 4.7mm
type_03=ratio:10%, pid:16777293, Item:270(wielded), Item:389, Script:1078 ; Enclave Sentry Bot MkII w/ RPG and Avenger Minigun
type_04=ratio:20%, pid:16777466, Item:28(wielded), Item:(0-50)41, Item:(0-1)39, Script:794, If(Rand(10%)) ; Enclave Patrol female w/ Gatling Laser and Large Energy Cell
type_05=ratio:20%, pid:16777467, Item:396(wielded), Item:(0-50)41, Item:(0-1)38, Script:794 ; Enclave Patrol male w/ YK32 Pulse Pistol and Small Energy Cell
type_06=ratio:10%, pid:16777467, Item:394(wielded), Item:(0-50)41, Item:(0-1)358, Script:794 ; Enclave Patrol female w/ PPK12 Gauss Pistol and 2mm EC
type_07=ratio:10%, pid:16777466, Item:955(wielded), Item:(0-50)41, Item:(0-1)362, Script:794 ; Enclave Patrol male w/ PPK12E Gauss Pistol and 4mm EC
;position=Surrounding
;position=straight_line, spacing:1
;position=straight_line, spacing:2
position=double_line, spacing:3
;position=wedge, spacing:2
;position=cone, spacing:2
;position=huddle, spacing:3
Pid: here you can specify critters, items (if its a container you can put stuff in it, if not don't), if its a critter, you can edit its inventory by adding the entry Item: followed by the PID for the item you want, if the item is their main weapon you can specify if its wielded, the last entries are Script: specify SID, and extra conditions like above there is a 10% random chance of this critter appearing.
after the critter entries you can specify the formation you want them to be placed in the encounter.
If you want to use a shortcut, just copy an existing encounter from the table that closely matches the type of encounter you want to create, copy it to the end of the randon encounter types list and give it a unique name and replace NPCs or edit their inventories to your liking.
Next look through the "Newly added Random Encounter Tables", the entries should look like this:
[Encounter Table 68]
lookup_name=Wild6_M ; Area between New Reno and NCR
maps=Mountain Encounter 1, Mountain Encounter 2, Cavern Encounter 0
enc_00=Chance:33%,Enc:(8-12) RED_Wolves AMBUSH Player
enc_01=Chance:33%,Enc:(8-12) DVMV_Mantis_Swarm AMBUSH Player
enc_02=Chance:33%,Enc:(8-12) DMRV_Scorpions AMBUSH Player
enc_04=Chance:25%,Enc:(2-5) Bounty_Hunter_Low AMBUSH Player, If(Global(1) > 1) And If(Player(Level) < 7)
enc_05=Chance:25%,Enc:(2-5) Bounty_Hunter_Low_Mid AMBUSH Player, If(Global(1) > 1) And If(Player(Level) > 6) And If(Player(Level) < 13)
enc_06=Chance:25%,Enc:(2-5) Bounty_Hunter_High_Mid AMBUSH Player, If(Global(1) > 1) And If(Player(Level) > 12) And If(Player(Level) < 19)
enc_07=Chance:25%,Enc:(2-6) Bounty_Hunter_High AMBUSH Player, If(Global(1) > 1) And If(Player(Level) > 18)
enc_08=Chance:25%,Enc:(2-4) Bounty_Hunter_Low AMBUSH Player, If(Global(0) < -500) And If(Player(Level) < 7)
enc_09=Chance:25%,Enc:(2-4) Bounty_Hunter_Low_Mid AMBUSH Player, If(Global(0) < -500) And If(Player(Level) > 6) And If(Player(Level) < 13)
enc_10=Chance:25%,Enc:(2-4) Bounty_Hunter_High_Mid AMBUSH Player, If(Global(0) < -500) And If(Player(Level) > 12) And If(Player(Level) < 19)
enc_11=Chance:25%,Enc:(2-5) Bounty_Hunter_High AMBUSH Player, If(Global(0) < -500) And If(Player(Level) > 18)
enc_11=Chance:20%,Enc:(4-7) Morton_Brother, If(Global(386) > 0) And If(Global(386) < 6)
enc_12=Chance:5%,Counter:1,Special,Map:Special Bridge Encounter,Enc:Special1, If(Player(Level) > 9) And If(Global(605) < 1)
enc_13=Chance:3%,Counter:1,Special,Map:Special Holy Encounter 2,Enc:Special1, If(Global(614) > 0) And If(Global(606) < 1)
Each table corresponds to an area in the worldmap, to add new encounters just edit the last line of the table that corresponds to the area where you want the encounter to happen, add the line with new encounter (ie: enc_14=Chance:25%,Enc:(6-10) New_Encounter_name AMBUSH Player) The first value is the encounter id, chance of finding encounter, number of critters in encounter, and encounter name. You can specify extra values like whether you want the encounter to appear when you have reached a certain level, etc.
Next you have to edit the text/english/game/Worldmap.msg, here all the encounter names are listed, just refer to the random encounter table of that corresponds to the table/s you edited and add the encounter name to the list, just make sure the number on the message index corresponds with the number you assigned to the encounter on that encounter table.
Hope this helps