With transaction /SCMTMS/BWIS you can selectively for the respective DataSources delete the entries in the setup tables, but you can't delete selectively on specific characteristics, only everything or nothing for the respective DataSources.
With transaction /SCMTMS/BWIU_TOR you can fill the setup tables for Transportation Orders. You can do this selectively for specific characteristics or all data at once. The DataSources involved can't be reduced. You update always DataSources 0SCM_TM_TOR, 0SCM_TM_TOR_ITM, 0SCM_TM_TOR_EXE, 0SCM_TM_TOR_STG, 0SCM_TM_TOR_TCD and 0SCM_TM_TOR_TDL together.
With transaction /SCMTMS/BWIU_TRQ you can fill the setup tables for Transportation Requests. Here you update always DataSources 0SCM_TM_TRQ, 0SCM_TM_TRQ_ITM and 0SCM_TM_TRQ_STG at once.
With transaction /SCMTMS/BWIU_SFIR you can fill the setup tables for the freight settlement documents. Here all five DataSources beginning with name 0SCM_TM_SFIR are updated.
With transaction /SCMTMS/BWIU_CFIR you can fill the setup tables for the forwarding settlement documents. Here all three DataSources beginning with name 0SCM_TM_SFIR are updated.
With transaction /SCMTMS/BWIU_BSH you can fill the setup table for the DataSource 0SCM_TM_BSH (BO Business Share).
With transaction /SCMTMS/BWIU_TAL you can fill the setup table for the DataSource 0SCM_TM_TAL (BO Transportation Allocation).
With transaction /SCMTMS/BWIU_FAG you can fill the setup table for the DataSource 0SCM_TM_FAG (BO Freight Agreement).
Only when the setup tables are filled, and you can check this for each DataSource using transaction rsa3 or using report RODPS_REPL_TEST in case ODP framework. Then you can do a full upload to your connected BW with this data.