Hi,
Question 1.: I guess you mean computations of the form ctensor[{...}, {...}]. In principle this should be handled by the function ReplaceMetric in your notebook. I mean, if you have an expression expr with metric factors that stay symbolic, try ReplaceMetric[expr, ...] and if this doesn't work then send an example.
Question 2.: When you work with an explicit metric (given as a CTensor object met) and a chart BL, then you need to use just CD = CovDOfMetric[met] and the derivative PDBL of BL. The derivative PD is there to play the role of abstract "partial derivative" associated to a generic chart, in the same way that the metric g defined with DefMetric[-1, g[-a, -b], cd] is a generic metric. Therefore we can work with generic abstract situations with g, cd, PD and then we can replace them respectively with met, CD, PDBL for concrete cases.
Cheers,
Jose.