Question: I am running Atlassian stash and I can see the Pull request option on the Web based UI, but I want to know if my users can create Pull requests from their consoles for their working copies without using the stash web UI ?

Answer: 
There are 2 Stash command line tools available:

<https://bitbucket.org/atlassian/stash-command-line-tools>

<https://marketplace.atlassian.com/plugins/org.swift.stash.cli>

Note that a pull request requires commits in a branch to be pushed rather than using the local working copy, and this works well in practice.
I have never done this, but it should be possible using the [Stash REST api](https://developer.atlassian.com/static/rest/stash/3.0.1/stash-rest.html) via some bash script or something to do the *POST*

> 
> **/rest/api/1.0/projects/{projectKey}/repos/{repositorySlug}/pull-requests**  
> 
>  This API can also be invoked via a user-centric URL when addressing
>  repositories in personal projects. Create a new pull request between
>  two branches. The branches may be in the same repository, or different
>  ones. When using different repositories, they must still be in the
>  same {@link Repository#getHierarchyId() hierarchy}.
> 
> 
> The authenticated user must have REPO\_READ permission for the "from"
>  and "to"repositories to call this resource.
> 
> 
> 

It sounds like quite some work, considering you will need to authenticate and all that, but it might still be worth it for you