Context. The classification of young stellar objects (YSOs) is typically done using the infrared spectral slope or bolometric temperature, but either can result in contamination of samples. More accurate methods to determine the evolutionary stage of YSOs will improve the reliability of statistics for the embedded YSO population and provide more robust stage lifetimes. Aims. We aim to separate the truly embedded YSOs from more evolved sources. Methods. Maps of HCO⁺J = 4-3 and C¹⁸O J = 3-2 were observed with HARP on the James Clerk Maxwell Telescope (JCMT) for a sample of 56 candidate YSOs in Perseus and Taurus in order to characterize the presence and morphology of emission from high density (n_crit > 10⁶ cm^-3) and high column density gas, respectively. These are supplemented with archival dust continuum maps observed with SCUBA on the JCMT and Herschel PACS to compare the morphology of the gas and dust in the protostellar envelopes. The spatial concentration of HCO⁺J = 4-3 and 850 μm dust emission are used to classify the embedded nature of YSOs. Results. Approximately 30% of Class 0+I sources in Perseus and Taurus are not Stage I, but are likely to be more evolved Stage II pre-main sequence (PMS) stars with disks. An additional 16% are confused sources with an uncertain evolutionary stage. Outflows are found to make a negligible contribution to the integrated HCO⁺ intensity for the majority of sources in this study. Conclusions. Separating classifications by cloud reveals that a high percentage of the Class 0+I sources in the Perseus star forming region are truly embedded Stage I sources (71%), while the Taurus cloud hosts a majority of evolved PMS stars with disks (68%). The concentration factor method is useful to correct misidentified embedded YSOs, yielding higher accuracy for YSO population statistics and Stage timescales. Current estimates (0.54 Myr) may overpredict the Stage I lifetime on the order of 30%, resulting in timescales down to 0.38 Myr for the embedded phase.