Most antispyware software lives quite nicely with other antispyware software. The ones you have to be careful with are the ones that have other features with them. For instance Lavasoft AdAware used to be a highly recommended antispyware removal tool, but then they combined it with an AntiVirus package. Now if you installed that and you had another Antivirus package installed, there would be conflict.
As for doing manual scans at different times, from the software's point of view there really is no reason to. But from a resource point of view, doing two at the same time will slow them both down. So it is best to run them individually.