I am not a Manifold user but if you can export your map into a tiff format you can then use Acrobat Professional or Nitro Reader (version 7 engine) to convert to PDF. Personally, I have never been able to successfully export a complex map (a combination of multiple raster and vector layers) to a PDF directly out of a GIS application. The only way is to export to Illustrator or CorelDRAW then convert the graphics to press quality PDF. (Extremely large files) To do this successfully for complex maps you might have to export the vectors and rasters separately then combine in post-processing.
The easiest way to get a decent output relatively small in file size is to export the map to tiff then convert to PDF with Acrobat Pro. If you don't have Acrobat Pro you can use Nitro but it must be newest Nitro Reader which uses the new rendering engine that will eventually be a part of the Nitro PDF Pro 7 if it ever comes out.
The Nitro Reader is the only software that (in my opionion) comes close to Acrobat when it comes to converting tiff to PDF.
Also I recommend not to use Nitro products to view the completed PDF on screen. The on-screen rendering is terrible in Nitro. Convert with Nitro Reader and view in the free Adobe Reader. Or just get Acrobat Pro.
I usually export to tiff at 300 - 400 DPI. My maps typically have several high resolution raster layers with transparencies, up to 50 vector layers and 5 - 30 annotation layers. When i export to tiff then convert such map to PDF using Acrobat Pro the resulting file is 1 - 2.5MB for a 11x17" map and 20 - 35MB for a ANSI E 34x44". The resulting image quality is very good but it is essentially a static image just packaged inside a PDF.