Hello Micaga,

Where can I find a template or instructions on how to organize and arrange data for 3D least square adjustment?

There is no template. Usually, the total station provides the observed measurements, e.g. a GSI file from Leica. In any case, the steps in JAG3D are:

1. create a project
2. import your data
3. define the adjustment type
4. specify the stochastic model
5. adjust the network
6. analysis the results

At sf.net, some sample data are provided taken from geodetic literature. Here, flat ASCII files are used for points and observations. The data of a very small 3D network can be found, for instance, in Baumann p. 230. A further (larger) network is given by Müller.

However, it is more easier to help you, if you specify your data.

regards
Micha