It’s tough to solve fitting dilemmas while your glue bonds with the wood, and there’s no going back after it has set. To keep yourself out of that bind, always dry-fit your assembly–that means no glue-to verify all joints fit together as planned. If joints don’t fit, go back and solve problems before applying glue.
Dry-fitting shows which clamps and how many are needed, and where on the assembly they go. You also get an idea of how long it will take to glue and clamp the assembly–you might discover that the process takes longer than the glue’s open time allows (typically less than 15 minutes for yellow glue). In that case, divide the work into sub-assemblies. For example, when building an end table, make two assemblies of two legs with their rails and let them dry, rather than trying to assemble all four legs and rails at the same time.