Hi ljstoot
1) It will probably be fine to use Ca44, and yes, if you use it as an internal standard with the normal trace elements DRS, you will not get a Ca44_ppm output. You know the Ca concentration since it was used as an internal standard.
2) I don't quite follow the question here, but each analysis (/selection) in the internal standards table can have its own element, value, and units. So, for example, if you select everything in the table and set the element to to Ca44, the NIST Ca concentrations should be automatically picked up from the reference material data, and so you will likely see those values in ppm (85000 ppm Ca). Values for your otolith will not be picked up automatically, so you would then select the subset of rows in that table corresponding to your otolith and set the units and value as desired (wtpc is fine).
All the best,