I should clarify my earlier answer (as on reviewing I didn't give a full response for which many apologies)-
This organisation gave 1 standard to each battalion (royal standard to the 1st & regimental standard to the 2nd carried by the Porta Bandeira) July 1808 – Regimento de Infanteria de Linha – 2 battalions, each of 5 companies (1 grenadier & 4 fusilier).
Regimental headquarters: 7 men
Coronel, Major (grade of Tenente Coronel), Quartel Mestre, Capellão, Cirurgião Mór, Coronheiro, Espingardeiro,
Battalion headquarters: 16 men
Chefe de batalho (grade of Major), Primeiro Ajudante (grade of Capitão), 4 Ajudantes de Cirurgião, Porta Bandeira, Cabo de Tambores, 8 Musicos,
Companies: 162 men
Capitao, Tenente, 2 Alferes, Primeiro Sargento, 2 Segundos Sargentos, Furriel, 8 Cabos, 2 Tambores, 144 Anspeçadas & Soldados.
This organisation appears to have consolidated the two battalion HQs into the regimental HQ so both standards would be centralised as per the diagram linked to by GarryWills – 1809 November – Regimento de Infantaria- headquarters augmented while companies remained as before.
Headquarters: 36 men.
Coronel, Tenente Coronel, 2 Majores, 2 Ajudantes, Thesoureiro (or Pagador), 2 Quarteis Mestres, 2 Sargentos de Brigada (or 2 Ajudantes Sargentos), 2 Quarteis Mestre Sargentos, 2 Porta-Bandeiras, Capellão, Cirurgião Mór, 4 Ajudantes do Cirurgião, Coronheiro, Espinguardeiro, Mestre de Musica, 8 Musicos, Tambor Mór, Cabo de Tambores, 2 Pifanos.
@forrester – definitely just 2 standards for the regiment.
@Frostie – Neither the infantry or the cavalry regiments of the Légion Portugaise were ever officially issued with flags or standards. From 1808 two Porte-Drapeau, flag bearers were included in the regimental budget and the funding may have been used to employ additional junior officers, but the application by Junot to have flags authorised for the infantry was postponed and then finally declined when the matter was raised again in 1811.