I have only done this once and I applied perspective correction in equal amounts prior to the stitch. I have only used a tripod once and it was such a problem setting up I have never done it before or since. I discovered that I can reduce the density of the upper layer to enable me to see the layer below to register hand held shots. In shooting with a generous overlap one can in an editing rather than stitch programme choose which version of reality one wants and can avoid shiowing people twice for example. In Paint Shop Pro, versions v.8 onwards, there is a tool called 'warp mesh' which places a grid of lines over the picture, you can decide how many you want either horizontally or vertically, and then move each intersecting point to correct or distort the image. One Photoshop advocate said it was worth getting PSP just for this tool, many of the PS Plug-ins cost as much and more back then when v.8 appeared
PSP is much cheaper too these days.