Observations of dense molecular gas lie at the basis of our understanding of the density and temperature structure of protostellar envelopes and molecular outflows. We aim to characterize the properties of the protostellar envelope, molecular outflow and surrounding cloud, through observations of high excitation molecular lines within a sample of 16 southern sources presumed to be embedded YSOs. Observations of submillimeter lines of CO, HCO+ and their isotopologues, both single spectra and small maps were taken with the FLASH and APEX-2a instruments mounted on APEX to trace the gas around the sources. The HARP-B instrument on the JCMT was used to map IRAS 15398-3359 in these lines. HCO+ mapping probes the presence of dense centrally condensed gas, a characteristic of protostellar envelopes. The rare isotopologues C18O and H13CO+ are also included to determine the optical depth, column density, and source velocity. The combination of multiple CO transitions, such as 3-2, 4-3 and 7-6, allows to constrain outflow properties, in particular the temperature. Archival submillimeter continuum data are used to determine envelope masses. Eleven of the sixteen sources have associated warm and/or dense quiescent as characteristic of protostellar envelopes, or an associated outflow. Using the strength and degree of concentration of the HCO+ 4-3 and CO 4-3 lines as a diagnostic, five sources classified as Class I based on their spectral energy distributions are found not to be embedded YSOs. The C18O 3-2 lines show that for none of the sources, foreground cloud layers are present. Strong molecular outflows are found around six sources, .. (continued in paper)
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