There is a specific place. If you scroll down through the .lua (I'm assuming you're doing conquest with Clone Wars, or XXXc_con.lua for this) you should see:
mission script wrote:ReadDataFile("dc:SIDE\\rep.lvl",
"snw_inf_wampa",
"rep_inf_ep3_rocketeer",
"rep_inf_ep3_engineer",
"rep_inf_ep3_sniper",
"rep_inf_ep3_officer",
"rep_inf_ep3_jettrooper",
"rep_hover_fightertank",
"rep_hero_anakin",
"rep_hover_barcspeeder")
ReadDataFile("SIDE\\cis.lvl",
"cis_inf_rifleman",
"cis_inf_rocketeer",
"cis_inf_engineer",
"cis_inf_sniper",
"cis_inf_droideka",
"CIS_inf_officer")
Depending on which side you want your jedi to be on, you would put dc: in front of that side. Now, instead of a jedi, I put in a modded wampa (lol), but where it says snw_inf_wampa, you would put jdi_demojedi (or whatever your side_jediname is). Then, further down in the .lua, you should see:
mission script wrote: SetupTeams{
rep = {
team = REP,
units = 32,
reinforcements = 150,
soldier = { "snw_inf_wampa", 9,25},
assault = { "rep_inf_ep3_rocketeer",1, 4},
engineer = { "rep_inf_ep3_engineer",1, 4},
sniper = { "rep_inf_ep3_sniper",1, 4},
officer = {"rep_inf_ep3_officer",1, 4},
special = { "rep_inf_ep3_jettrooper",1, 4},
},
cis = {
team = CIS,
units = 10,
reinforcements = -1,
soldier = { "CIS_inf_rifleman",9, 25},
assault = { "CIS_inf_rocketeer",1, 4},
engineer = { "CIS_inf_engineer",1, 4},
sniper = { "CIS_inf_sniper",1, 4},
officer = { "CIS_inf_officer",1, 4},
special = { "cis_inf_droideka",1, 4},
and again, where i put the wampa, you would put jdi_demojedi. Munge all that up and you should be good (unless there are other, unrelated problems, which

)