The homebrew package you wish to install should be a file with the .vpk extension.
Make sure Wifi is enabled and you are connected to the same network as the host computer.
Open molecularShell by launching the bubble.
Press SELECT to start a FTP server. Please note that the FTP server is not password protected. Only run it on a trusted local network.
Note the IP address displayed in a message popup.
Open your FTP client on the host computer and connect to that IP address. (for FileZilla just type in the vita's IP into the box labeled host)
Navigate to ux0 (this is the root of your memory card) and you can upload the .vpk package here or in any subdirectory.
Once you upload all the packages you wish to install you can disconnect the client.
Back in molecularShell, press CIRCLE to stop the FTP server.
Navigate to ux0: and then to where you placed the packages. To install, select the package and press X.