Look at the CRIRES telescope allocation schedule. Check that your targets are not too close to the Moon (at least 30 degrees away). If they are very close then the telescope Active Optics and/or CRIRES Adaptive Optics will not work.
Remember to prepare a backup program in case of poor seeing, clouds or strong winds. If the wind speed is higher than 12 m/s then the telescope needs to point at least 90 degrees away. Note that the North/South cutoff is at DEC = -24.6 deg and the wind normally (not always) comes from the North. To do this fill out this web form. Recall that without prior-approval, only targets in your Phase 1 proposal can be observed. For this reason, send the backup request well in advance and not at the last minute when it may be impossible to approve. Recall that the VLT cannot observe through the zenith so take care in scheduling observations of sources with declinations within 3 degrees of -24.6.
Read the User manual! In particular, note that: (1) Normally 3 darks, 3 flatfields and a wavelength calibration are taken the morning after your observations. You can ask your Night Astronomer to do more and/or change the DIT/NDIT combination of the Darks. (2) AO observations with thick cloud are not allowed due to the high risk of damaging the Avalanche Photo Diodes. (3) If SEQ.NGS.USELASTSKY is set to 'F' you need to be sure that the sky position chosen (by default 4 arcseconds East and 4 arcseconds North) is free of stars. Otherwise, damage to the APDs may result. The offset values can be changed. (4) AO stars must be fainter than R=0.2 magnitude and brighter than R=15.
Check that the line of interest compared with telluric features (using the exposure time calculator) and make sure that it is covered by the relevant setting. Remember CRIRES wavelength coverage is not continuous and that between 2 (Y-band) and 9 (M-band) settings are needed to cover an entire band.
Visitor gas cells are not accepted. Only the two installed gas cells can be used for simultaneous wavelength calibration.
Quick-look reduced data will be available of your observations. However, these should not be used for science purposes, as they are processed with static (old) calibrations. You should obtain your data from the archive archive.eso.org using the calSelector option to associate the calibrations nearest in time to your observations. Note that the reduced data will not contain any information on the radial velocity.
A data reduction cookbook does not yet exist for the upgraded CRIRES. For data reduction using the original CRIRES pipeline a cookbook is available on the manuals page here