The short answer Alex is;
1. assign the software token to your user (whom you either manually create in the Internal database, or import / point to in an external Identity Source e.g. Active Directory)
2. Distribute the assigned soft token (based on a Token Profile you created earlier - to define things such as device type;iPhone, Droid, or Windows PC, and format e.g. CTF, CTKIP or .sdtid file.
3. Deliver the CTF string or .sdtid file to the end user, e.g. email (hopefully secure email or something within your LAN)
4. End User imports token into the software token app running on their device (smart phone or Windows PC typically)
The AM Admin Guide has details on assigning tokens, creating token Profiles and distributing soft tokens (some older docs refer to 'issuing' software tokens but that is same concept)
If you need to setup an external Identity source to Active Directory or Sun/Oracle or Open LDAP, there was a discussion on this site with links to a PowerPoint on that
Software token software (aka app) can be downloaded from your phone store or for PCs from RSA sites such as this one, RSA Link
The Quick Start Guide for a device will explain how to import tokens
The attached PowerPoint attempts to explain various Soft Token concepts
