>>I have proposed that they have some links running down the right hand side of the page<<
>>reasons for putting them on the side was to bring them up higher in the page source code<<
My understanding of how a typical bot reads a page is:
main content, if done in < p > or equivalent fashion.
then Footer/ nav / bottom, whatever.
If you are using tables:
If content is in Tables: Left column, top to bottom. Next col. top to bottom, etc., like a newspaper col.
Then content below table in fashion as above < p >, etc.
then Footer / bottom, etc.
So, if you are using tables and placing your links in a table in the last column to the right this would be picked up next to last by a bot, just before footer (or more content below table). Yes, they would be higher up in the source code relative to the bottom but but still near end of code.
This is my understanding anyway from years past. I don't know how exactly google reads a page. I may be wrong on this but welcome any corrections, comments.
You wish to check out the html forum as well.