The .cho file only contains the choice data, so you would need to import a CSV file of the non-choice data in order to use the filters. This would be done in SMRT by going to File -> Merge Variables -> Add.
It might be easier, however, to filter the data before making the .cho file. We released a data cleaner tool back for version 6 that allows you to set up a filter file and clean up the .dat file. It's towards the bottom of our Downloads page at http://www.sawtoothsoftware.com/support/downloads.
The data cleaner will allow you to create a clean .cho file and run the logit model in SMRT. However, if you have a license for CBC/HB, we would recommend running the data through that to get individual-level utilities and use those in simulations.
The current version of the software has all the analysis options (counts, logit, Latent Class, HB) embedded in SSI Web and is a lot easier to use. The next version will also replace SMRT with a simulator inside SSI Web. You would qualify for a 40% discount on the upgrade, and essentially get Latent Class and HB for free, with a free upgrade to version 9 when it is released. Send an e-mail to email@example.com if you are interested in an upgrade quote.