WRT Offline Effects: You can reach these via the "Offline Effects" menu in the main menu bar of Music Studio. Make sure that you have an audio object selected/highlighted in your arrangement first, so the programs knows what object to apply this effect to. Keep in mind that these are destructive effects.
As far as your questions about and problems with your multi-track recording session are concerned, please observe the following guidelines and tips:
First of all, in order to avoid recording latency related timing/sync problems, please make sure you're working with ASIO drivers. Go into the program settings of Music Studio (e.g. by pressing "Y" on your keyboard) and switch to ASIO as your driver model. Then pick a functional ASIO driver from the "ASIO Device" drop-down list. This could be the ASIO driver that was supplied with your sound hardware or it might be a generic ASIO driver like ASIO4ALL or the "Magix Low Latency" driver that comes with Music Studio.
Now try recording again and see how this has affected the recording latency. It's most likely fine now and recording latency is down to just a negligible period of time. If it comes down to it, you might have to optimize your system a little for improved audio performance. If you don't have a proper, dedicated sound card yet, you might want to install one. A decent sound card is such an important element of home recording that I can't really recommend using the crummy on-board sound solutions that are basically just designed to turn office machines into somewhat more flexible gaming and multi-media systems. If you're serious about your music and home recording, you might want to spend at least $100 to $200 on your sound card, as far as I'm concerned.
Make sure you configure your Windows/sound card mixer in a manner that it will only perform recordings from the actual input socket that you feed your signal into (e.g. mic or line). Mute other sources that are not relevant at the time of recording. Otherwise, you will obviously just get one big mess. Use headphones for monitoring while you're recording your additional tracks, so you don't have a speaker-to-microphone loop, or something like that.
Well, I hope the information above is relevant to the problem you've been experiencing and you can get it sorted. If you're still having problems, you might have to provide some more details.