Hydraulic parameters for an aquifer flow can be expressed on different terms like Hydraulic Conductivity (K) or Transmissivity (T). On the default setup of MODFLOW 2005 with Model Muse there is no option to use directly Transmissivity unless a manual conversion is done to transform into K, this is because the selected flow package is Layer Property Flow (LPF).
When the flow package changes to Block Centered Flow (BCF6) it is possible to insert Transmissivities directly as datasets or as a object property. The BCF package also has more options for the layer type, with unconfined and partial confined aquifer options.
This quick tutorial show the procedure to change the flow package in Model Muse and setup Transmissivities by layers and as object property.