How to render faster with 3d effects?

A 2-hour render for a 2 minute sequence with keying and 3d effects might well be about right.  When you say you render it part by part, that suggests to me that your computer might be struggling with the effects involved and you've had to split it to get any output.  As Mylenium says it does depend a lot on your system and what resources After Effects can draw on.

If you are not extruding or bending layers, use the Classic 3D render mode. It is faster.

Without seeing the timeline with the modified properties of all 3D layers, it is impossible to give you any meaningful suggestions. 2 minutes is a very long time for one shot. If there are cuts between shots in the video, I strongly recommend that you make every comp a single shot. The longer the composition, the higher the likelihood that resources will get used up and the render will slow down. The only time I have more than one shot in the composition is when I am creating a transition between shots that cannot be made in any other way. 

Possible slowdowns include unnecessary motion blur, Motion Tile, Particle systems, Keying effects, Rotobrush, Warp Stabilizer, Grow Bounds, and any effect that utilizes the GPU combined with other effects that use the GPU. Sometimes they cancel each other out. 

When I have render problems, I start by selecting suspect layers, pressing the 'u' key twice, and looking for things I can simplify or even turn off. The new Render Time column in the timeline can help identify problems. 

Two hours to render a two-minute composition may not be unreasonable. I often create composites that take about a minute a frame. When the render time starts approaching 2 minutes a frame, I redesign. 

One more suggestion: I often pre-render using the Composition menu when I have done something to a layer that I know will increase render time or bloat my project file dramatically. Rotobrush is almost always pre-rendered. The total time to render the project can be significantly decreased by pre-rendering problematic layers when the effects are compounding render time. Some footage formats will also dramatically increase the render time. MPEG files can be especially slow to decode.

You don't. There is no magic "make faster" button anywhere. If you care to divulge specific details about your system, effects and functions used, the effect settings and so on we may be able to advise, but quite generally you will simply have to get used to those render times. It's just how AE works and 2 hours for 2 minutes of content really isn't that bad. Even if there is potential to optimize it may shave off 10 minutes, but that could easily end up spending longer on tweaking effect settings than it is worth just letting AE render the stuff...

Mylenium