ok this is what I have picked up from other forums on this
when you pwned the device and open cydia (if done last couple days) you will get a message asking to update cydia, when its done and you close it then reopen again it re-organises things to give you space for apps.
You can also specify size of the partition for apps via pwnage tool in advanced mode, I have mine set to 1gig had a worry when cydia updated and said running low on disk space but I have been fine since it updated and reorganised things