Apply a playback offset to the MIDI track that drives the offending synthesizer, or bounce the synthesizer output to disk, and then import the audio into your arrangement where you can line it up with the rest of your tracks. Programs like Nemesys' GigaSampler and GigaStudio come with optimized, dedicated drivers, so check that your soundcard is compatible with the drivers of all your potential software instruments. If you'd prefer separate outputs or a digital interface, you can choose among the plethora of soundcards made by Sonorus, Digidesign, Echo, M Audio, MOTU, Korg, etc. Unless you dedicate one or more computers to your soft synths, you'll run them within the same machine that hosts your audio sequencer. Several systems allow you to connect these two types of programs, the main ones being Propellerhead Rewire, Digidesign Direct Connect, MOTU MAS 2.0, and Steinberg VST 2.0.
Performance can vary.
For instance, Rebirth offers flawless synchronization with Cubase via ReBirth, but Koblo Gamma 9000 falters. It will be interesting to see if Propellerhead's forthcoming Rewire 2.0 will up the ante. The Vibra9000 has a great multimode filter, and separate outputs for the lowpass, bandpass and highpass signal. In most cases, these hardware platforms are open to third-party development. But these solutions are more expensive, and third-party offerings are less abundant.