Following is a summary of the questions you have asked. 

Is there anyway I can configure the system so that I can have a template in terms of graph parameters such as range of data to be fit? 

The range of data to be fit can be set by using the variables MKS1 and MKS2. MKS1 is the starting row number and MKS2 is the ending row number. For example, if you have 100 datapoints, but only want to fit rows 10 though 85, use the following:

MKS1=10; //Set beginning of range
MKS2=85; //Set end of range

Axis configuration?

Axis configurations are saved with graph templates. You can set the properties of the graph such as colors, layer size and location, text labels, plot types, axis rescale properties, and many other properties. Once this template has been saved, you can open the template with the LabTalk commands window -t or page -t.

Can the boltzman function can be passed to my data without having to specify each time the same parameters?

To perform the Bolzman sigmoidal fitting, you can use the following command:

run.section(fit,Sigmoidal); //performs a sigmoidal fit on the current data selection

If you want to set the default parameters for the Bolzman function, go into the fitfunc subdirectory of Origin41. Open bolzman.fdf with a text editor. You can now edit the Initial Values line.

A short script which would use these features would look like:

window -t templatefilename.otp; //open template
layer -i Data1_B; //Add dataset to layer
mks1=10; //set begin range
mks2=85; //set end range
run.section(fit.Sigmoidal); //run sigmoidal fitting script