Do i need to convert my sequence to PIR file format in order to use it.
If by "use it", you mean you want to build a comparative model, then yes.
If yes, how do i do it??
PIR files are just plain text, so they're very easy to make manually in
a text editor or with some simple scripting.
Is it recommended to generate alignment from external sources and then
perform modelling using modeller or I can generate my model for a
sequence using only modeller.
You can do it either way. The alignment you use for modeling doesn't
have to be generated by Modeller.