Most stars born in clusters and recent results suggest that star formation (SF) preferentially occurs in subclusters. Studying the morphology and SF history of young clusters is crucial to understanding early SF. We identify the embedded clusters of young stellar objects (YSOs) down to M stars, in the HII regions RCW33, RCW32 and RCW27 of the Vela Molecular Ridge. Our aim is to characterise their properties, such as morphology and extent of the clusters in the three HII regions, derive stellar ages and the connection of the SF history with the environment. Through public photometric surveys such as Gaia, VPHAS, 2MASS and Spitzer/GLIMPSE, we identify YSOs with IR, Halpha and UV excesses, as signature of circumstellar disks and accretion. In addition, we implement a method to distinguish M dwarfs and giants, by comparing the reddening derived in several optical/IR color-color diagrams assuming suitable theoretical models. Since this diagnostic is sensitive to stellar gravity, the procedure allows us to identify pre-main sequence stars. We find a large population of YSOs showing signatures of circumstellar disks with or without accretion. In addition, with the new technique of M-type star selection, we find a rich population of young M stars with a spatial distribution strongly correlated to the more massive population. We find evidence of three young clusters, with different morphology. In addition, we identify field stars falling in the same region, by securely classifying them as giants and foreground MS stars. We identify the embedded population of YSOs, down to about 0.1M_{sun}_, associated with the HII regions RCW33, RCW32 and RCW27 and the clusters Vela T2, Cr197 and Vela T1, respectively, showing very different morphologies. Our results suggest a decreasing SF rate in Vela T2 and triggered SF in Cr197 and Vela T1.