Stephen said the truth…*too many unknowns…*but I will attempt a generic outline.
Yes. Different. Firstly colour settings must be set to the output intent. RGB for untagged I set to rRGB irrespective of bridge or other Adobe applications. Images that are to be colour managed should prefereably be in RGB for maximum flexibility.
Next step is open the file, on question about RGB enable all profiles if there is a missmatch, (if there is a profiler use it if no profile you will now have sRGB).
When question about CMYK comes up, it depends on the job. If moving from one coated to another coated profile I prefer ignore profiles to avoid contamination and/or black colour conversions.
I actually use convert to output intent and preserve numbers irrespective of if I export to PDFx1a or PDFx4, this is safest way to work. The job is tagged and will proof with output intent, but will not have strange things happen in the rip if printed in different sites. TAC can be verified and don't need to think about if digial proofer has different black point configuration.
If the job is for newsprint or uncoated then it's trickier to know when to convert CMYK and when to preserve values. If illustrations are of a technical nature usually safe CMYK (preserving values) is better, but brand colours such as oranges and blues will need to have magenta adjusted, if the original artwork is intended for Coated. This is a routine that needs to be considered with the customer. An alternative is to use Acrobat for converting PDF's of artwork from coated to uncoated as Acrobat colour converter allows preserving blacks. (For this reason some jobs for uncoated may be treated as coated and colour managed with a device link at RIP)
There are exceptions to the rule, but this is the flow I find safe for most jobs, irrespective of workflow.
