Ive been wondering about this for a while now, so ive decided to put my questions down on a blog.
When Urahara first meets Isshin after Isshin kills Grand Fisher, it appears that they know each other quite well... with urahara even knowing about the death of masaki. It is also implied that Urahara has something to do with Isshin's giving up of his powers, as he states that he hopes Isshin doesnt blame him if he has become weaker.... i suspect that Urahara probably made him a Gigai which supressed his reiatsu and this aspect may have appeared to weaker isshin. So at this point it appears that they are at least old colleagues, if not friends. However what i find interesting is that Urahara lies to Isshin as seen on this page ( http://www.onemanga.com/Bleach/188/09/ ) , when Isshin talks of the Vizard he refers to them as criminals attempting to illegally gain hollow powers, and Urahara does not inform him that this is not the true story. So it makes me wonder why Urahara did not tell Isshin the full story, does Urahara not trust Isshin, is Urahara hiding something? i just found it quite weird considering the language they use makes them sound like allies in the upcoming fight with Aizen.